AtlasCreator for 3D Slicer
Version v0.21
3D Slicer manually specified: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --tmp_dir /var/tmp/haehn --config_dir /var/tmp/haehn
Created output directory: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/
Debug Mode is enabled!
Adding module path: /var/tmp/haehn/Slicer3haehn/16139/CMTK4Slicer
Starting Slicer: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build
[AtlasCreator 11:47:50] --------------------------------------------------------------------------------
[AtlasCreator 11:47:50] Starting Atlas Creator Normal Mode
[AtlasCreator 11:47:50] Configuration for Atlas Creator:
Original Images: ['/projects/na-mic/haehn/DATASETS/Study/originals/case10.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case12.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case14.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case15.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case19.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case2.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case20.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case23.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case26.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case27.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case29.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case3.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case32.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case33.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case36.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case40.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case41.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case42.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case46.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case47.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case48.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case51.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case53.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case54.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case57.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case59.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case60.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case61.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case62.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case8.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG1.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG10.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG11.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG12.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG13.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG14.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG15.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG16.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG17.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG2.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG27.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG3.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG33.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG4.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG5.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG6.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG7.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG8.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG9.nrrd']
Segmentations: ['/projects/na-mic/haehn/DATASETS/Study/segmentations/case10.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case12.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case14.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case15.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case19.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case2.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case20.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case23.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case26.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case27.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case29.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case3.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case32.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case33.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case36.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case40.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case41.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case42.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case46.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case47.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case48.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case5.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case51.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case53.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case54.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case57.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case59.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case60.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case61.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case62.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case8.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG1.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG10.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG11.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG12.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG13.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG14.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG15.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG16.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG17.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG2.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG27.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG3.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG33.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG4.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG5.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG6.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG7.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG8.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG9.nrrd']
Output Directory: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/
Template Type: dynamic
Dynamic Template Iterations: 5
Fixed Template Default Case:
Labels: [32, 3, 4, 5, 6, 7, 8, 9, 10, 31]
Toolkit: BRAINSFit
Registration Type: Affine
Save Transforms: 1
Delete Aligned Images: 0
Delete Aligned Segmentations: 0
Normalize Atlases: 0
Output Cast: Short
[AtlasCreator 11:47:50] Entering Registration Stage..
[AtlasCreator 11:47:50] Found 3D Slicer launcher at /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3
[AtlasCreator 11:47:50] DEBUG: The launchCommandPrefix is /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/
[AtlasCreator 11:47:50] Dynamic registration with 5 iterations
[AtlasCreator 11:47:50] Starting iteration 1...
Background level guess :
first place: 0 (99.6492%)
second place: 68 (0.00519283%)
Guessed background level: 0
[AtlasCreator 11:48:13] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 11:48:15] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 11:48:15] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
218 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 127
LowHigh Thresholds: [0,44.0234,127]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2a1f750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.994522 0.103956 -0.0109262
-0.104528 0.989074 -0.103956
-8.67362e-19 0.104528 0.994522
Offset: [-1.10284, 0.332162, -3.67198]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-0.530611, -1.53524, -3.00189]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.103956 0.989074 0.104528
-0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, -0.00273905, -0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997673 0.0681781 -0.000582901
-0.0681566 0.997059 -0.0350414
-0.00180787 0.0349996 0.999386
Offset = [-1.08895, -0.578494, -2.03424]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.9926 0.0504959 -0.0082426
-0.0506719 0.996493 -0.0227488
0.00708115 0.0231367 0.860429
Offset = [-0.927372, -0.499219, 0.871226]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.977129 0.0382417 -0.009361
-0.0261312 0.986737 -0.092614
-0.00881105 0.0439931 0.810328
Offset = [-1.23029, 0.594611, 2.26756]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.973595 0.030788 -0.0142023
-0.0237396 0.982346 -0.0815964
0.00053473 0.0488199 0.798335
Offset = [-1.14549, 0.470202, 2.45625]
Background level guess :
first place: 0 (99.8355%)
second place: 156 (0.00356523%)
Guessed background level: 0
[AtlasCreator 11:52:34] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 11:52:35] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 11:52:35] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
269 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,64.1875,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x13ba750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 -1.45062e-18
1.38778e-17 0.994522 0.104528
0 -0.104528 0.994522
Offset: [-0.361738, -0.982522, -2.10076]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-0.361738, 0.971294, -2.9799]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 -0.104528
-1.45062e-18 0.104528 0.994522
Singular: 0
Versor: [ -0.052336, -3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999005 -0.0122471 0.0428744
0.0105018 0.999116 0.0406986
-0.0433349 -0.0402078 0.998251
Offset = [-1.28059, 0.990336, -1.73155]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.955468 0.00580698 0.0362262
-0.00754332 0.998196 0.0479794
-0.0359048 -0.0482203 0.920057
Offset = [-1.36825, 0.810064, -0.149428]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924026 -0.0101182 0.0187782
0.00130744 0.980015 -0.00889222
-0.0402376 -0.0483051 0.806027
Offset = [-1.24546, 1.44365, 2.57687]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.930814 0.00785759 0.0108562
-0.00690817 0.987398 -0.0171194
-0.0317318 -0.0455385 0.807121
Offset = [-1.0449, 1.18786, 2.54227]
Background level guess :
first place: 0 (99.1645%)
second place: 142 (0.0144934%)
Guessed background level: 0
[AtlasCreator 11:56:56] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 11:56:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 11:56:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
261 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 167
LowHigh Thresholds: [0,59.6953,167]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1343750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.987688 -0.15622 0.00818715
0.156434 0.986335 -0.0516916
0 0.052336 0.99863
Offset: [-1.21864, 0.38676, 0.0582395]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-2.1969, -0.995689, 0.419931]
Inverse:
0.987688 0.156434 0
-0.15622 0.986335 0.052336
0.00818715 -0.0516916 0.99863
Singular: 0
Versor: [ 0.0260963, 0.00205382, 0.0784322, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.994231 -0.0952568 0.0493123
0.0971976 0.994517 -0.0385758
-0.0453673 0.0431462 0.998038
Offset = [-2.43478, -0.0573223, 0.971187]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 73 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.936021 -0.0816021 0.0597185
0.083504 1.00069 -0.0300729
-0.0570288 0.0349055 0.830834
Offset = [-3.34559, -0.253364, 4.84237]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 75 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.925343 -0.0863551 0.0795876
0.106739 0.999659 -0.0525511
-0.0906986 0.0330374 0.809146
Offset = [-3.81826, 0.390861, 5.34092]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.925003 -0.0804074 0.09481
0.111973 0.997755 -0.0701313
-0.109309 0.0496399 0.801536
Offset = [-3.98915, 0.384831, 5.81492]
Background level guess :
first place: 0 (99.9963%)
second place: 141 (0.00031002%)
Guessed background level: 0
[AtlasCreator 12:01:38] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:01:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:01:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
377 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.8906,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1343750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 -0.0163519
-0.104528 0.982278 -0.155578
0 0.156434 0.987688
Offset: [-1.38496, 3.23737, 2.86292]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-0.921543, 0.334658, 3.78728]
Inverse:
0.994522 -0.104528 0
0.103242 0.982278 0.156434
-0.0163519 -0.155578 0.987688
Singular: 0
Versor: [ 0.0783516, -0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998399 0.0519331 -0.0224318
-0.0534667 0.995804 -0.0742659
0.0184809 0.0753463 0.996986
Offset = [-1.22474, 1.50869, 3.74715]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 171 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.948123 0.0484574 -0.0365554
-0.0508906 0.945141 -0.0688616
0.0330843 0.0705949 0.837524
Offset = [-1.05444, 2.08667, 6.88654]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.92665 0.0501423 -0.041943
-0.0496307 0.930934 -0.0775419
0.030588 0.0618662 0.783318
Offset = [-1.11434, 2.29124, 8.51409]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.926234 0.0589732 -0.0406325
-0.0630042 0.923354 -0.0838069
0.0346772 0.0660271 0.773999
Offset = [-1.31115, 2.17243, 8.88426]
Guessed background level: 0
[AtlasCreator 12:05:53] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:05:54] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:05:54] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case19.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case19.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case19.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
331 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 220
LowHigh Thresholds: [0,81.1562,220]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xb00750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4054
Debug: Off
Observers:
none
Matrix:
0.994522 0.104385 0.0054706
-0.104528 0.993159 0.0520493
-8.67362e-19 -0.052336 0.99863
Offset: [5.18153, 2.21144, -0.0469903]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [6.06979, 3.3509, -0.460979]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.104385 0.993159 -0.052336
0.0054706 0.0520493 0.99863
Singular: 0
Versor: [ -0.0261411, 0.00137, -0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998595 0.0524855 0.00731006
-0.0524893 0.998621 0.000336459
-0.00728232 -0.000719686 0.999973
Offset = [5.48076, 3.56184, 0.0157157]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 144 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.939802 0.0317065 -0.00239662
-0.0317005 0.932071 0.00251555
0.00247516 -0.0024383 0.86697
Offset = [5.5846, 3.74442, 3.1912]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908232 0.0506882 0.0238831
-0.0441985 0.898773 -0.0411889
-0.0210421 0.00507621 0.777929
Offset = [4.60638, 4.36358, 5.73998]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904658 0.0466059 0.00133098
-0.0401673 0.897302 -0.0490372
-0.0138689 0.0100757 0.774622
Offset = [5.18202, 4.1773, 5.87225]
Background level guess :
first place: 0 (99.9893%)
second place: 41 (0.00031002%)
Guessed background level: 0
[AtlasCreator 12:10:17] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:10:18] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:10:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
245 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 157
LowHigh Thresholds: [0,57.2812,157]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e5b750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
0.994522 0.104385 0.0054706
-0.104528 0.993159 0.0520493
-8.67362e-19 -0.052336 0.99863
Offset: [-0.483217, -6.83908, -9.38176]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [0.405045, -5.69962, -9.79575]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.104385 0.993159 -0.052336
0.0054706 0.0520493 0.99863
Singular: 0
Versor: [ -0.0261411, 0.00137, -0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996109 0.0706583 -0.0526625
-0.0668846 0.995283 0.0702713
0.0573794 -0.0664756 0.996137
Offset = [0.326861, -6.69559, -8.57945]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 85 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.953148 0.043848 -0.0790133
-0.0389925 0.924407 0.0619809
0.0815189 -0.0586464 0.837009
Offset = [1.0674, -5.17576, -5.29466]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.946842 0.0455339 -0.0712128
-0.0751144 0.903816 0.0202123
0.052455 -0.0756779 0.799915
Offset = [0.492049, -4.69604, -4.3313]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93748 0.0457732 -0.0680928
-0.0726473 0.909736 -0.00216746
0.0542498 -0.069587 0.77884
Offset = [0.376199, -4.37864, -3.65861]
Background level guess :
first place: 0 (99.9754%)
second place: 87 (0.000697545%)
Guessed background level: 0
[AtlasCreator 12:14:26] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:14:27] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:14:27] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case20.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case20.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case20.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
274 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,64.5469,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x191d750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [-1.44956, -2.3202, 7.93671]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-0.907704, 0.657889, 6.54253]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99991 0.0130191 0.00329749
-0.0132991 0.994063 0.107987
-0.00187203 -0.108021 0.994147
Offset = [-0.894379, -1.32733, 7.78026]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 69 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995829 0.0215271 -0.0148757
-0.0203002 0.952804 0.0782069
0.0165106 -0.0778781 0.829523
Offset = [-1.2506, -0.874992, 11.2764]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.990614 -0.00789134 -0.066121
0.0488415 0.940129 0.0495283
0.0635695 -0.0721365 0.797989
Offset = [-0.282977, -0.228097, 13.3291]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.986256 0.00316725 -0.0519451
0.0455661 0.944164 0.0507556
0.0488511 -0.0759798 0.789526
Offset = [-0.529025, -0.266112, 13.1425]
Guessed background level: 0
[AtlasCreator 12:18:32] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:18:33] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:18:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case23.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case23.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case23.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 181
LowHigh Thresholds: [0,64.5703,181]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1cc9750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.54598, -1.00305, -5.78979]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [1.54598, 2.80199, -7.74748]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999906 0.0129898 -0.00446905
-0.0117417 0.977031 0.212772
0.00713028 -0.2127 0.977092
Offset = [1.734, -1.04438, -5.6523]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 59 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996682 0.00465563 -0.0236329
0.000149461 0.940837 0.199366
0.0240866 -0.199312 0.842562
Offset = [1.60071, -0.360069, -2.65804]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.984618 -0.00442019 -0.00848154
8.50629e-05 0.925936 0.150092
0.00858542 -0.19495 0.794859
Offset = [1.44302, 0.897826, -1.46123]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.968624 0.0108309 -0.0121203
-0.000735814 0.916385 0.140619
0.0168273 -0.198055 0.756524
Offset = [1.19372, 0.797402, -0.257633]
Background level guess :
first place: 0 (99.606%)
second place: 143 (0.00759549%)
Guessed background level: 0
[AtlasCreator 12:22:32] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:22:33] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:22:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case26.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case26.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case26.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
259 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 171
LowHigh Thresholds: [0,61.1719,171]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xc57750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104385 -0.0054706
0.104528 0.993159 0.0520493
4.33681e-19 -0.052336 0.99863
Offset: [-5.03785, -3.18721, -8.08155]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-5.90546, -2.44185, -8.49554]
Inverse:
0.994522 0.104528 4.33681e-19
-0.104385 0.993159 -0.052336
-0.0054706 0.0520493 0.99863
Singular: 0
Versor: [ -0.0261411, -0.00137, 0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 64 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995465 -0.0750839 0.0584097
0.0733802 0.996829 0.0307893
-0.0605363 -0.0263635 0.997818
Offset = [-6.45662, -2.23919, -7.72946]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 54 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
1.00874 -0.0551742 0.0228347
0.0546272 1.00524 0.0239231
-0.024114 -0.022633 0.85562
Offset = [-6.29493, -2.34133, -4.19462]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.981655 -0.0819573 0.0237317
0.0866162 0.989034 -0.0218886
-0.0463616 -0.0296744 0.829028
Offset = [-6.71333, -1.88476, -3.31659]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.991249 -0.0856791 0.00994067
0.0887355 0.998135 -0.0132979
-0.0464956 -0.0271457 0.833633
Offset = [-6.38137, -1.89523, -3.46778]
Background level guess :
first place: 0 (99.9778%)
second place: 228 (0.00093006%)
Guessed background level: 0
[AtlasCreator 12:26:42] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:26:43] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:26:43] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
340 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 240
LowHigh Thresholds: [0,89.9062,240]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xac5750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104528 1.45062e-18
0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [-0.739036, 3.05866, -12.8679]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-1.50333, 2.82101, -12.8679]
Inverse:
0.994522 0.104528 0
-0.104528 0.994522 1.38778e-17
1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, 3.63154e-19, 0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 44 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996362 -0.084566 0.0105992
0.0842393 0.996047 0.0281948
-0.0129416 -0.0271993 0.999546
Offset = [-1.35026, 2.09458, -12.1939]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 69 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93054 -0.0718958 0.0240024
0.0710175 0.942373 0.0356356
-0.0264886 -0.0338285 0.845421
Offset = [-1.94618, 2.62632, -9.14622]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.889005 -0.0666168 0.0223367
0.053292 0.916829 -0.00121313
-0.032969 -0.0207337 0.73738
Offset = [-2.40781, 3.44331, -6.18111]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.893195 -0.0719002 0.0242256
0.0571777 0.917601 -0.00308378
-0.036675 -0.0142992 0.735872
Offset = [-2.38479, 3.33388, -6.16282]
Guessed background level: 0
[AtlasCreator 12:30:44] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:30:45] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:30:45] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case29.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case29.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case29.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
228 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 172
LowHigh Thresholds: [0,62.9062,172]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xf07750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [-6.13368, 0.420075, -7.99866]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-6.13368, 4.22511, -9.95635]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999999 -0.000805119 -0.00115004
0.00101193 0.9812 0.19299
0.000973043 -0.192991 0.9812
Offset = [-6.33929, 0.713772, -8.24088]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 85 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.925896 0.00252372 0.000745989
-0.00260478 0.920299 0.14386
-0.000375165 -0.143861 0.824337
Offset = [-6.64696, 2.08194, -4.15432]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.922815 -0.00786517 -0.0203424
-0.0138415 0.904796 0.121084
0.0464942 -0.184126 0.821804
Offset = [-6.182, 2.68104, -3.82378]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.913075 -0.0112256 -0.0274286
-0.0340913 0.90667 0.0965933
0.0291279 -0.190796 0.802345
Offset = [-6.27332, 3.21492, -3.7074]
Background level guess :
first place: 0 (99.6932%)
second place: 135 (0.00364273%)
Guessed background level: 0
[AtlasCreator 12:34:48] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:34:49] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:34:49] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
324 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,69.3359,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2435750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-5.56428, 4.01606, -3.74289]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-5.56428, 0.940036, -2.81853]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 71 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
1 -1.94954e-05 -0.000367907
-5.25921e-06 0.997742 -0.0671652
0.000368386 0.0671652 0.997742
Offset = [-5.80369, 1.47519, -1.54695]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 94 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928192 -0.0176443 -0.0375105
0.0153015 0.975634 -0.0618515
0.0385256 0.0612244 0.798414
Offset = [-5.1214, 1.90146, 2.50692]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920321 -0.0219779 -0.0277417
0.0209585 0.971633 -0.0702325
0.0172547 0.039255 0.782581
Offset = [-5.33419, 1.90333, 2.66432]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 81 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921505 -0.0138617 -0.047077
0.0047886 0.98037 -0.0751755
0.0371851 0.0363238 0.784382
Offset = [-5.14073, 2.0183, 2.51905]
Background level guess :
first place: 0 (99.9661%)
second place: 125 (0.00100756%)
Guessed background level: 0
[AtlasCreator 12:39:17] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:39:18] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:39:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case32.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case32.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case32.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
253 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 162
LowHigh Thresholds: [0,58.4531,162]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2528750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 -0.0108813
0.052336 0.976807 0.207627
8.67362e-19 -0.207912 0.978148
Offset: [-1.29913, -2.87552, -11.0259]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-1.88352, 0.81548, -12.9836]
Inverse:
0.99863 0.052336 8.67362e-19
-0.0511923 0.976807 -0.207912
-0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, -0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.9978 -0.035259 -0.056143
0.0458981 0.978469 0.201224
0.0478392 -0.203359 0.977935
Offset = [-0.75794, -2.47035, -10.3058]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 63 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.943359 -0.0183255 -0.0601974
0.0301322 0.972129 0.201527
0.0552413 -0.202942 0.840309
Offset = [-1.12011, -2.30807, -6.90718]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 96 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.914877 -0.0421617 -0.0737801
0.043783 0.945602 0.124848
0.0418239 -0.208776 0.775939
Offset = [-0.652464, -0.208068, -5.09885]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904168 -0.0273553 -0.0656447
0.038271 0.947248 0.125471
0.0459983 -0.207678 0.780678
Offset = [-1.14343, -0.6964, -5.38784]
Guessed background level: 0
[AtlasCreator 12:43:33] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:43:34] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:43:34] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
224 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 144
LowHigh Thresholds: [0,52.8125,144]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x279f750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [4.97971, -5.61507, -14.294]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [5.56927, -1.72674, -16.2517]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 98 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998919 0.0449649 -0.0117619
-0.042282 0.984238 0.171722
0.019298 -0.171039 0.985075
Offset = [5.44255, -4.31785, -13.7337]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.972916 0.0574322 -0.0343937
-0.0509117 0.934744 0.167201
0.043467 -0.165075 0.880644
Offset = [5.74865, -3.77668, -11.213]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 149 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.938308 0.0428252 -0.0395459
-0.0464949 0.916277 0.0532208
0.0334046 -0.158446 0.822627
Offset = [5.53394, -1.96091, -10.1648]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.937052 0.0447937 -0.0530939
-0.0584194 0.917387 0.044961
0.0388241 -0.157537 0.812374
Offset = [5.43176, -1.95233, -9.5778]
Background level guess :
first place: 0 (99.8568%)
second place: 144 (0.00224764%)
Guessed background level: 0
[AtlasCreator 12:48:14] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:48:15] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:48:15] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case36.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case36.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case36.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
273 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,63,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x237a750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
0.978148 -0.206773 -0.0217327
0.207912 0.972789 0.102244
-1.73472e-18 -0.104528 0.994522
Offset: [-3.72155, -1.16907, -11.9026]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-5.62732, 0.188168, -12.7817]
Inverse:
0.978148 0.207912 -1.73472e-18
-0.206773 0.972789 -0.104528
-0.0217327 0.102244 0.994522
Singular: 0
Versor: [ -0.0520493, -0.0054706, 0.104385, 0.993159 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.987698 -0.155995 0.0108906
0.153816 0.981725 0.112061
-0.0281725 -0.109007 0.993642
Offset = [-4.76306, -1.78947, -11.0187]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.925689 -0.161942 0.0541049
0.153632 0.986326 0.132888
-0.074497 -0.122624 0.825041
Offset = [-6.17805, -1.68809, -7.20785]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.913768 -0.164734 0.036304
0.142953 0.975417 0.0843332
-0.0747863 -0.116858 0.789933
Offset = [-5.93047, -0.601352, -6.37248]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915949 -0.158784 0.0330264
0.140246 0.979093 0.0739146
-0.0681525 -0.119921 0.770525
Offset = [-5.71778, -0.513635, -5.35282]
Background level guess :
first place: 0 (99.9645%)
second place: 127 (0.000697545%)
Guessed background level: 0
[AtlasCreator 12:52:09] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:52:10] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:52:10] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case40.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case40.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case40.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 204
LowHigh Thresholds: [0,73.7344,204]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2797750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 -2.17096e-18
1.38778e-17 0.987688 0.156434
-1.92593e-34 -0.156434 0.987688
Offset: [3.17878, -3.78591, -14.6929]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [3.17878, -0.89236, -16.0871]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.37069e-17 0.987688 -0.156434
-2.17096e-18 0.156434 0.987688
Singular: 0
Versor: [ -0.0784591, -5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999426 0.0308651 -0.013959
-0.0289015 0.991875 0.12389
0.0176694 -0.123415 0.992198
Offset = [2.985, -2.74606, -14.6736]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.961977 0.0370193 -0.0518528
-0.0305904 0.971252 0.119712
0.0558871 -0.117882 0.930965
Offset = [3.26175, -2.47482, -12.9914]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 111 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.926925 0.0187825 -0.033847
-0.00110173 0.942143 0.0274207
0.0128146 -0.103483 0.803061
Offset = [2.95094, -0.0998339, -10.2697]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 63 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.914541 0.0344258 -0.0436525
-0.0194444 0.934566 0.0396921
0.0282518 -0.111288 0.785228
Offset = [2.98524, -0.586338, -9.47264]
Background level guess :
first place: 0 (99.8872%)
second place: 69 (0.00271267%)
Guessed background level: 0
[AtlasCreator 12:56:34] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 12:56:35] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 12:56:35] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case41.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case41.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case41.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 139
LowHigh Thresholds: [0,50.0625,139]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1ec7750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 0.0054706
-0.052336 0.993159 0.104385
-8.67362e-19 -0.104528 0.994522
Offset: [-3.3899, -1.13118, -12.3205]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-2.89722, 0.908466, -13.1997]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0520493 0.993159 -0.104528
0.0054706 0.104385 0.994522
Singular: 0
Versor: [ -0.052318, 0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999428 0.00401139 0.0335774
-0.00892631 0.989016 0.147536
-0.0326168 -0.147751 0.988487
Offset = [-3.56089, -1.53865, -11.6017]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920991 0.00798547 0.00999609
-0.00886386 0.972399 0.0911587
-0.00922613 -0.0912399 0.794923
Offset = [-4.15019, -0.402503, -7.07791]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 68 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.917895 0.00737792 0.0347048
-0.0309025 0.952288 0.0231004
-0.0567645 -0.0884296 0.787903
Offset = [-4.40981, 0.412771, -6.86602]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.923242 0.00213125 0.0168414
-0.0280489 0.962361 0.0402107
-0.0609408 -0.102972 0.778
Offset = [-3.89952, -0.253008, -6.64716]
Guessed background level: 0
[AtlasCreator 13:00:50] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:00:51] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:00:51] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case42.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case42.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case42.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,70.1172,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1911750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 -2.17096e-18
1.38778e-17 0.987688 0.156434
-1.92593e-34 -0.156434 0.987688
Offset: [0.343873, -2.09019, -20.0487]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [0.343873, 0.803354, -21.4429]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.37069e-17 0.987688 -0.156434
-2.17096e-18 0.156434 0.987688
Singular: 0
Versor: [ -0.0784591, -5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999982 -0.00192141 0.00566875
0.000911765 0.984921 0.173
-0.00591568 -0.172992 0.984906
Offset = [0.247807, -2.15652, -18.7619]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.935543 0.0186642 -0.011712
-0.0163527 0.956253 0.173353
0.0147686 -0.17312 0.844941
Offset = [0.216638, -1.6175, -16.1204]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.91328 -0.000753424 -0.0161098
-0.0278369 0.933965 0.105429
-0.00525595 -0.175474 0.760489
Offset = [0.0321327, -0.467607, -13.9615]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905137 0.00516674 -0.0092938
-0.0390457 0.939448 0.100996
-0.000810673 -0.166842 0.761156
Offset = [-0.170853, -0.316689, -13.5008]
Background level guess :
first place: 0 (99.7911%)
second place: 120 (0.00356523%)
Guessed background level: 0
[AtlasCreator 13:04:53] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:04:54] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:04:54] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case46.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case46.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case46.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
226 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,54.4219,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2565750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [5.11007, 3.6593, -3.39099]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [4.9409, -0.572771, -2.26718]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998581 -0.0421218 0.0325821
0.0473417 0.98235 -0.180962
-0.0243846 0.182247 0.98295
Offset = [4.38252, 2.91785, -2.70425]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.938911 -0.0146596 0.0549286
0.024294 0.953538 -0.179078
-0.0513989 0.180123 0.827516
Offset = [3.5243, 2.73022, 0.621935]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.938173 -0.0280239 0.0374132
0.0126544 0.95329 -0.166064
-0.0654909 0.169998 0.81392
Offset = [3.80764, 2.803, 1.06099]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 79 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932709 -0.00960289 0.0148644
-0.0152824 0.949674 -0.171927
-0.0610177 0.171725 0.805033
Offset = [4.58338, 2.80961, 1.68717]
Guessed background level: 0
[AtlasCreator 13:09:03] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:09:04] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:09:04] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case47.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case47.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case47.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
287 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,63.25,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xb6c750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [-5.40484, -1.76123, -1.30489]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-5.68359, -3.90227, -0.634799]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 60 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999922 0.00727712 0.0101312
-0.0066241 0.997988 -0.0630621
-0.0105698 0.0629901 0.997958
Offset = [-6.4, -3.48131, -0.833519]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.951351 -0.0149325 0.013314
0.0159692 0.896817 -0.0815051
-0.012051 0.0817014 0.861735
Offset = [-6.42474, -2.01645, 2.44137]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.943797 -0.000744677 0.017275
0.0248551 0.885615 -0.0693234
-0.0418683 0.0661699 0.800998
Offset = [-6.49954, -1.99835, 4.32139]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.935283 0.00195781 0.0124808
0.0177108 0.891959 -0.0837738
-0.0364618 0.0804938 0.805549
Offset = [-6.62048, -2.01005, 4.23303]
Guessed background level: 0
[AtlasCreator 13:13:05] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:13:07] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:13:07] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case48.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case48.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case48.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
205 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 133
LowHigh Thresholds: [0,47.8047,133]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xa97750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.987688 0.156434 -2.17096e-18
-0.156434 0.987688 -1.37069e-17
-1.92593e-34 1.38778e-17 1
Offset: [0.217093, -0.979642, -12.3893]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [1.39957, -0.775978, -12.3893]
Inverse:
0.987688 -0.156434 -1.92593e-34
0.156434 0.987688 1.38778e-17
-2.17096e-18 -1.37069e-17 1
Singular: 0
Versor: [ 6.9175e-18, -5.44419e-19, -0.0784591, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.989912 0.138665 -0.0290812
-0.138655 0.990338 0.00235837
0.0291273 0.00169769 0.999574
Offset = [1.00103, -0.582801, -11.4818]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 63 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.974375 0.112612 -0.0173637
-0.112023 0.921146 0.0318496
0.0208322 -0.029697 0.8698
Offset = [1.09542, -0.76155, -8.33878]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 117 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.961945 0.0652529 -0.0427306
-0.0360211 0.915722 -0.0611171
0.0330706 -0.0164577 0.787927
Offset = [1.10963, 1.24583, -6.58319]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.958374 0.0744966 -0.0438221
-0.0453778 0.916856 -0.0744967
0.0357804 -0.0215032 0.78038
Offset = [0.755318, 1.44803, -6.40437]
Background level guess :
first place: 0 (99.7032%)
second place: 148 (0.00596788%)
Guessed background level: 0
[AtlasCreator 13:17:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:17:30] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:17:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,63.2109,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1350750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [1.52831, 1.66029, -18.6598]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [2.07017, 4.63838, -20.054]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999576 0.0283159 0.00681567
-0.0290024 0.989154 0.143988
-0.00266461 -0.144124 0.989556
Offset = [1.41164, 2.12967, -18.5763]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.978702 0.0408415 0.0428804
-0.046599 1.00355 0.143228
-0.0365415 -0.144975 0.908799
Offset = [0.486001, 2.25662, -16.7504]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.967084 0.0245997 0.0156302
-0.0541343 0.99683 0.106443
-0.0399914 -0.150734 0.853086
Offset = [1.02113, 2.8023, -15.2531]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.97251 0.033068 0.020677
-0.0617265 0.986019 0.100901
-0.0287528 -0.156336 0.844549
Offset = [0.79847, 3.00223, -14.6499]
Background level guess :
first place: 0 (99.5194%)
second place: 159 (0.00658792%)
Guessed background level: 0
[AtlasCreator 13:21:22] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:21:23] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:21:23] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case51.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case51.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case51.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
265 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 174
LowHigh Thresholds: [0,63.7031,174]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xbb2750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [2.26481, 0.900748, 5.30145]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [2.26481, -3.22816, 6.42525]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998875 0.0265999 0.0392666
-0.0209941 0.990371 -0.136841
-0.0425284 0.135862 0.989815
Offset = [0.969901, -0.637837, 6.68059]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 131 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928557 0.013175 0.0266166
-0.00959976 0.992033 -0.130242
-0.0281045 0.129929 0.857723
Offset = [1.14623, -0.0960176, 9.34886]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915417 0.020486 0.0271707
-0.0224517 0.972986 -0.135112
-0.0364391 0.128929 0.824768
Offset = [1.03746, -0.273858, 10.1899]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.912424 0.0191749 0.0218798
-0.0316317 0.976657 -0.136463
-0.0362721 0.126945 0.830889
Offset = [0.900947, -0.491511, 10.5378]
Background level guess :
first place: 0 (99.921%)
second place: 111 (0.00124008%)
Guessed background level: 0
[AtlasCreator 13:25:42] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:25:43] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:25:43] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case53.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case53.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case53.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 195
LowHigh Thresholds: [0,72.1875,195]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2286750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 0.0522642 -0.00273905
-0.052336 0.997261 -0.0522642
-6.50521e-19 0.052336 0.99863
Offset: [1.7379, 1.18808, -8.58147]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [2.07553, 0.26924, -8.21978]
Inverse:
0.99863 -0.052336 -6.50521e-19
0.0522642 0.997261 0.052336
-0.00273905 -0.0522642 0.99863
Singular: 0
Versor: [ 0.026168, -0.000685233, -0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998701 0.0424351 -0.0281988
-0.0426439 0.999067 -0.00684497
0.027882 0.00803859 0.999579
Offset = [2.05898, 0.253176, -7.44972]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 163 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.967201 0.0469843 -0.0208991
-0.047458 0.96763 -0.0227793
0.0197999 0.023741 0.838589
Offset = [1.51548, 1.65193, -3.88698]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.958075 0.0513554 -0.0211784
-0.0526027 0.950702 -0.0632101
-0.00707892 0.0182045 0.810514
Offset = [1.31705, 2.48442, -3.16791]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.955733 0.0453252 -0.0127332
-0.0513527 0.954542 -0.0624773
-0.0161649 0.0225121 0.819095
Offset = [1.35883, 2.25406, -3.07485]
Guessed background level: 0
[AtlasCreator 13:30:06] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:30:07] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:30:07] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case54.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case54.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case54.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
295 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 196
LowHigh Thresholds: [0,73.4062,196]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1bf7750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 -2.17096e-18
1.38778e-17 0.987688 0.156434
-1.92593e-34 -0.156434 0.987688
Offset: [-2.59724, 1.8597, -4.61893]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-2.59724, 4.75325, -6.01311]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.37069e-17 0.987688 -0.156434
-2.17096e-18 0.156434 0.987688
Singular: 0
Versor: [ -0.0784591, -5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999984 0.00555783 -0.000965155
-0.00534971 0.988632 0.150259
0.0017893 -0.150252 0.988646
Offset = [-2.80097, 1.99508, -4.23027]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 112 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.952595 0.00160373 0.0119167
-0.0029246 0.897731 0.111667
-0.011663 -0.111694 0.891167
Offset = [-3.64469, 3.6679, -2.56554]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.916699 -0.00682153 0.0228111
-0.00416139 0.868523 0.0521837
-0.0431438 -0.115146 0.786817
Offset = [-3.54319, 4.99889, -0.413252]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.901256 0.00294833 0.0141324
-0.0201088 0.867455 0.0545801
-0.0345077 -0.135062 0.742081
Offset = [-3.33206, 4.8956, 1.43898]
Background level guess :
first place: 0 (99.8487%)
second place: 86 (0.00263517%)
Guessed background level: 0
[AtlasCreator 13:34:15] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:34:16] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:34:16] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case57.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case57.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case57.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
264 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 169
LowHigh Thresholds: [0,60.8125,169]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1484750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 1.45062e-18
1.38778e-17 0.994522 -0.104528
0 0.104528 0.994522
Offset: [-1.521, 0.947541, -1.69457]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-1.521, -1.08747, -1.02447]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 0.104528
1.45062e-18 -0.104528 0.994522
Singular: 0
Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999343 -0.0229959 0.0280292
0.0252728 0.996163 -0.0837855
-0.025995 0.0844388 0.99609
Offset = [-2.07204, 0.379313, -1.0395]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 146 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.956847 -0.0291177 0.00320583
0.0292641 0.95972 -0.0646591
-0.00131503 0.0647251 0.843561
Offset = [-1.86003, 0.628295, 2.41737]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.941017 -0.0186918 0.0237909
0.0332791 0.93907 -0.113849
-0.0268877 0.0815681 0.772293
Offset = [-2.50209, 1.75373, 3.97809]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932413 -0.0125467 0.0221746
0.0197781 0.939673 -0.11141
-0.0283737 0.0746563 0.767521
Offset = [-2.46574, 1.50683, 4.07897]
Guessed background level: 0
[AtlasCreator 13:38:26] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:38:27] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:38:27] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case59.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case59.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case59.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,70.0312,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xc25750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
0.994522 0.104528 -1.45062e-18
-0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [1.60409, -1.18945, -5.14372]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [2.38904, -1.033, -5.14372]
Inverse:
0.994522 -0.104528 0
0.104528 0.994522 1.38778e-17
-1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, -3.63154e-19, -0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995745 0.0921173 0.00240727
-0.0921078 0.995742 -0.00380549
-0.00274757 0.00356757 0.99999
Offset = [1.34913, -1.25715, -4.78785]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 78 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.965606 0.065682 0.00512133
-0.0656347 0.938211 -0.00892988
-0.00569662 0.00857434 0.889582
Offset = [1.16052, -0.272748, -2.13202]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93582 0.0526262 0.000440248
-0.0225039 0.920379 -0.0515449
-0.0240912 0.0173904 0.796791
Offset = [1.30945, 0.755212, -0.177526]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.935299 0.0600667 -0.00337162
-0.0398064 0.918352 -0.0481586
-0.0301183 0.0237345 0.794775
Offset = [1.186, 0.567378, 0.181565]
Guessed background level: 0
[AtlasCreator 13:42:24] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:42:26] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:42:26] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case60.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case60.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case60.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
338 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 239
LowHigh Thresholds: [0,90.25,239]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xc4a750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 0.0054706
-0.052336 0.993159 0.104385
-8.67362e-19 -0.104528 0.994522
Offset: [-1.84966, -1.27205, -2.26409]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-1.35698, 0.767596, -3.14323]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0520493 0.993159 -0.104528
0.0054706 0.104385 0.994522
Singular: 0
Versor: [ -0.052318, 0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997607 0.0545388 -0.0424997
-0.0512088 0.995803 0.0758508
0.0464581 -0.073493 0.996213
Offset = [-0.847941, -0.43452, -1.67583]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.972765 0.0290419 -0.0523953
-0.0259213 0.97366 0.0592864
0.0540073 -0.0578218 0.919581
Offset = [-0.8518, -0.149676, -0.29428]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.923167 0.0423946 -0.0561412
-0.0373418 0.918181 0.0146275
0.0558802 -0.062662 0.791732
Offset = [-1.06251, 1.37927, 2.52849]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.896669 0.0379691 -0.0572639
-0.0430982 0.913459 0.00425875
0.0489517 -0.0701013 0.74084
Offset = [-1.47823, 1.31144, 3.61143]
Background level guess :
first place: 0 (99.929%)
second place: 112 (0.00186012%)
Guessed background level: 0
[AtlasCreator 13:46:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:46:30] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:46:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case61.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case61.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case61.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,53.9062,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x29be750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-0.991761, -0.475551, 2.5852]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-1.16093, -4.70762, 3.709]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 70 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999405 -0.0041318 0.034256
0.0119338 0.972925 -0.230813
-0.0323749 0.231084 0.972395
Offset = [-2.18012, -0.518388, 3.25578]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 143 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.984131 -0.0237649 0.0485483
0.034358 0.919476 -0.230659
-0.0417282 0.23199 0.829182
Offset = [-2.44423, -0.439834, 5.98882]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.974543 -0.00848836 0.0694537
0.0396224 0.914966 -0.242178
-0.0764441 0.242899 0.805033
Offset = [-2.79197, 0.0416168, 6.50102]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.966944 -0.0105296 0.0400354
0.0355311 0.907595 -0.243664
-0.0652923 0.243858 0.787891
Offset = [-2.29438, -0.101796, 6.86435]
Background level guess :
first place: 0 (99.9685%)
second place: 147 (0.000852555%)
Guessed background level: 0
[AtlasCreator 13:50:55] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:50:56] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:50:56] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case62.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case62.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case62.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
252 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,62.1562,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xde4750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4054
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 -1.45062e-18
1.38778e-17 0.994522 0.104528
0 -0.104528 0.994522
Offset: [-3.16913, 2.29059, -1.38575]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-3.16913, 4.24441, -2.26489]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 -0.104528
-1.45062e-18 0.104528 0.994522
Singular: 0
Versor: [ -0.052336, -3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999621 -0.0275133 -2.00004e-06
0.0275133 0.999621 0.000162064
-2.45963e-06 -0.000162057 1
Offset = [-3.18604, 4.20805, -1.11875]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 91 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.958006 0.0160062 -0.0243051
-0.0153713 0.906396 0.026085
0.0247115 -0.0257003 0.814336
Offset = [-3.15256, 4.3429, 2.84382]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.940547 -0.0449732 -0.0394819
0.0475745 0.908658 -0.0442491
0.0100556 -0.0133929 0.777505
Offset = [-2.91162, 5.53716, 3.41071]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.939279 -0.0314973 -0.02915
0.032191 0.915811 -0.0439308
0.00311057 -0.0142994 0.77535
Offset = [-3.33968, 5.4645, 3.92656]
Background level guess :
first place: 0 (99.5161%)
second place: 137 (0.00713046%)
Guessed background level: 0
[AtlasCreator 13:55:08] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:55:09] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:55:09] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/case8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
263 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 160
LowHigh Thresholds: [0,58.2422,160]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x181e750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 1.45062e-18
1.38778e-17 0.994522 -0.104528
0 0.104528 0.994522
Offset: [0.533305, -1.13354, 5.46382]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [0.533305, -3.16855, 6.13391]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 0.104528
1.45062e-18 -0.104528 0.994522
Singular: 0
Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998921 -0.0215281 -0.0411574
0.0196659 0.998788 -0.0451279
0.042079 0.0442698 0.998133
Offset = [0.938103, -1.74867, 6.76493]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 102 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.870531 -0.0415182 -0.0379997
0.0399567 0.997989 -0.0409682
0.0396383 0.0393849 0.830963
Offset = [0.456146, -1.41884, 10.5899]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 63 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.852956 -0.0312132 -0.006141
0.0179988 0.987726 -0.0764112
-0.0111765 0.0426191 0.774806
Offset = [-0.182358, -1.36433, 11.7505]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.853187 -0.0304066 -0.0360414
0.0225232 0.986765 -0.0701199
0.0152281 0.0325858 0.772096
Offset = [0.510441, -1.51342, 12.0342]
Background level guess :
first place: 0 (99.7564%)
second place: 38 (0.00302269%)
Guessed background level: 0
[AtlasCreator 13:59:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 13:59:26] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 13:59:26] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG1.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG1.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG1.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
347 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 234
LowHigh Thresholds: [0,86.4844,234]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1273750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.994522 0.104385 -0.0054706
-0.104528 0.993159 -0.0520493
4.33681e-19 0.052336 0.99863
Offset: [1.16611, -1.90202, 3.1273]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [1.84561, -2.74877, 3.48899]
Inverse:
0.994522 -0.104528 4.33681e-19
0.104385 0.993159 0.052336
-0.0054706 -0.0520493 0.99863
Singular: 0
Versor: [ 0.0261411, -0.00137, -0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.994881 0.0514847 -0.0869531
-0.0556697 0.99737 -0.0464094
0.0843351 0.0510125 0.995131
Offset = [2.63855, -1.41325, 4.44654]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93467 0.0441854 -0.0833752
-0.0458405 0.982049 -0.0180414
0.0824768 0.0217829 0.870699
Offset = [2.61526, -1.81129, 7.21751]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.929578 0.0409316 -0.0959682
-0.0220406 0.978289 -0.0150483
0.0893843 0.0264646 0.838445
Offset = [2.68908, -1.8437, 7.68563]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 59 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93241 0.0442766 -0.101456
-0.0262377 0.975222 -0.0192683
0.0821032 0.0254936 0.828028
Offset = [2.93406, -1.83629, 8.05109]
Background level guess :
first place: 0 (99.7627%)
second place: 186 (0.00410776%)
Guessed background level: 0
[AtlasCreator 14:03:35] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:03:36] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:03:36] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 215
LowHigh Thresholds: [0,80.8828,215]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2a0d750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104385 0.0054706
0.104528 0.993159 -0.0520493
-8.67362e-19 0.052336 0.99863
Offset: [4.27218, 1.77919, 14.6428]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [3.61333, 0.538335, 15.0045]
Inverse:
0.994522 0.104528 -8.67362e-19
-0.104385 0.993159 0.052336
0.0054706 -0.0520493 0.99863
Singular: 0
Versor: [ 0.0261411, 0.00137, 0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998571 -0.0376232 -0.0379562
0.0353222 0.997599 -0.0595739
0.0401064 0.0581481 0.997502
Offset = [4.31502, 2.23863, 15.1521]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.958104 -0.0675482 -0.031879
0.0653757 0.993953 -0.0648719
0.0361255 0.0626066 0.919797
Offset = [3.92759, 2.53856, 16.8751]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924112 -0.0612306 -0.0465187
0.0435166 0.958177 -0.123105
0.0287715 0.0583614 0.800917
Offset = [4.16378, 3.71371, 19.4263]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 55 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915048 -0.0627214 -0.0387133
0.0463474 0.956983 -0.114695
0.0150809 0.0487061 0.789441
Offset = [3.67133, 3.23484, 19.761]
Background level guess :
first place: 0 (99.8225%)
second place: 6 (0.00767299%)
Guessed background level: 0
[AtlasCreator 14:07:38] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:07:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:07:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG11.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG11.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG11.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.7344,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x15f3750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
0.99863 0.052336 -7.26307e-19
-0.052336 0.99863 -1.38588e-17
0 1.38778e-17 1
Offset: [3.39504, -2.68963, 7.97473]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [3.78547, -2.60112, 7.97473]
Inverse:
0.99863 -0.052336 0
0.052336 0.99863 1.38778e-17
-7.26307e-19 -1.38588e-17 1
Singular: 0
Versor: [ 6.93652e-18, -1.81639e-19, -0.0261769, 0.999657 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999454 0.0288534 0.016092
-0.0280561 0.998466 -0.0477413
-0.0174448 0.0472638 0.99873
Offset = [2.98352, -1.73793, 7.61397]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 97 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932066 0.0148563 0.0469635
-0.0125975 0.962189 -0.0480332
-0.0476191 0.0473833 0.88276
Offset = [2.01937, -1.05197, 10.2281]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.917231 0.0136186 0.0123965
-0.00600869 0.955524 -0.0788077
-0.0541973 0.052134 0.831711
Offset = [2.76711, -0.456138, 11.4592]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905246 0.000126866 0.00704194
-0.000320676 0.94678 -0.0689887
-0.0374996 0.0434606 0.805258
Offset = [2.62171, -0.943888, 12.3746]
Guessed background level: 0
[AtlasCreator 14:11:40] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:11:41] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:11:41] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
321 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.5,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xedf750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
0.99863 -0.052336 7.26307e-19
0.052336 0.99863 -1.38588e-17
0 1.38778e-17 1
Offset: [-0.66939, -0.519891, -0.458886]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-1.05465, -0.628707, -0.458886]
Inverse:
0.99863 0.052336 0
-0.052336 0.99863 1.38778e-17
7.26307e-19 -1.38588e-17 1
Singular: 0
Versor: [ 6.93652e-18, 1.81639e-19, 0.0261769, 0.999657 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 134 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999764 0.00825207 0.0200818
-0.00799938 0.999888 -0.0126312
-0.0201837 0.0124676 0.999719
Offset = [-1.58204, -0.511116, 0.121544]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 83 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898002 -0.0145127 0.0129776
0.0144298 0.911681 0.00645492
-0.0130697 -0.00626643 0.809871
Offset = [-1.95428, 0.732486, 4.39944]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 70 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.882022 -0.013093 0.0267273
-0.00545367 0.906856 -0.0435833
-0.0592607 -0.0138865 0.75482
Offset = [-2.44261, 1.26922, 5.47678]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878941 -0.00332728 0.00674361
-0.0181837 0.901114 -0.0608529
-0.0468853 -0.00571373 0.7414
Offset = [-1.92769, 1.5291, 6.0784]
Background level guess :
first place: 0 (99.7555%)
second place: 81 (0.00325521%)
Guessed background level: 0
[AtlasCreator 14:16:15] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:16:17] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:16:17] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG13.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG13.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG13.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.0938,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1497750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0522642 0.00273905
0.052336 0.997261 -0.0522642
4.33681e-19 0.052336 0.99863
Offset: [-0.638511, -0.0665706, 10.0757]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-0.970975, -1.18274, 10.4374]
Inverse:
0.99863 0.052336 4.33681e-19
-0.0522642 0.997261 0.052336
0.00273905 -0.0522642 0.99863
Singular: 0
Versor: [ 0.026168, 0.000685233, 0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999186 -0.0243612 0.0321446
0.0257592 0.998707 -0.0438209
-0.0310355 0.0446132 0.998522
Offset = [-1.3839, -0.233298, 10.6321]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.960819 -0.0184035 0.0326832
0.0195923 0.970336 -0.0364341
-0.0319847 0.0370488 0.828535
Offset = [-2.07535, -0.14497, 14.8556]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.952989 -0.0242607 0.0505656
0.0329709 0.965756 -0.0661455
-0.0697282 0.0324047 0.801222
Offset = [-2.17068, 0.656312, 15.524]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.953143 -0.0200297 0.0469263
0.0324506 0.97018 -0.0522335
-0.0721567 0.0285014 0.810284
Offset = [-2.27309, 0.225011, 15.4513]
Background level guess :
first place: 0 (98.828%)
second place: 187 (0.0134859%)
Guessed background level: 0
[AtlasCreator 14:20:03] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:20:05] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:20:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
348 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,80.2812,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x29f1750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.47401, 3.40682, 11.0616]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [3.47401, -0.722089, 12.1854]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99989 0.00890906 0.01188
-0.00654869 0.982587 -0.185687
-0.0133275 0.185588 0.982537
Offset = [2.7346, 3.21601, 11.8881]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 92 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.966916 0.00686157 -0.00639452
-0.00799509 0.981943 -0.198624
0.00490404 0.198667 0.880357
Offset = [2.4858, 3.22729, 14.3855]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.959049 0.00349118 0.0116889
0.0159506 0.984175 -0.16728
-0.0601017 0.171004 0.865406
Offset = [2.69409, 2.81451, 14.7715]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 67 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.95382 0.000645036 0.00479426
0.0124898 0.990592 -0.176947
-0.0647711 0.183248 0.870492
Offset = [2.77898, 2.47453, 14.8356]
Background level guess :
first place: 0 (99.838%)
second place: 81 (0.00387525%)
Guessed background level: 0
[AtlasCreator 14:24:22] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:24:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:24:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 186
LowHigh Thresholds: [0,69.8438,186]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x287d750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 -0.0108813
0.052336 0.976807 0.207627
8.67362e-19 -0.207912 0.978148
Offset: [1.08148, -5.44214, -3.96806]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [0.497079, -1.75114, -5.92575]
Inverse:
0.99863 0.052336 8.67362e-19
-0.0511923 0.976807 -0.207912
-0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, -0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999741 -3.39671e-05 -0.0227413
0.00265975 0.993311 0.115443
0.0225852 -0.115474 0.993054
Offset = [0.631286, -3.18458, -4.39004]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.988876 -0.0169493 -0.0377074
0.0219645 0.990473 0.136844
0.0350241 -0.137555 0.945381
Offset = [1.01833, -3.53824, -3.11327]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.962749 -0.0268571 -0.0192378
0.08975 0.968847 0.0782625
0.0212882 -0.15963 0.886375
Offset = [0.371549, -2.09838, -1.80603]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 146 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.95812 -0.0218297 -0.0370189
0.0874944 0.958367 0.0486288
0.00901979 -0.144955 0.841634
Offset = [0.698914, -1.93281, -0.634067]
Guessed background level: 0
[AtlasCreator 14:28:47] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:28:49] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:28:49] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG16.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG16.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG16.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 225
LowHigh Thresholds: [0,84.6094,225]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e48750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
1 -1.38588e-17 7.26307e-19
1.38778e-17 0.99863 -0.052336
0 0.052336 0.99863
Offset: [-1.62605, 0.284457, -6.10826]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-1.62605, -0.724273, -5.74657]
Inverse:
1 1.38778e-17 0
-1.38588e-17 0.99863 0.052336
7.26307e-19 -0.052336 0.99863
Singular: 0
Versor: [ 0.0261769, 1.81639e-19, 6.93652e-18, 0.999657 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99973 0.00344042 -0.0229608
-0.00419331 0.999452 -0.0328232
0.0228353 0.0329106 0.999197
Offset = [-1.30313, -0.777543, -5.78746]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 73 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915947 -0.0186288 -0.0548102
0.0166814 0.905716 -0.0357768
0.055434 0.0348025 0.829618
Offset = [-0.969754, 0.243544, -1.79509]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.888042 -0.0222962 -0.029666
0.0457196 0.874934 -0.0793139
0.0142806 0.0186153 0.744657
Offset = [-1.96577, 1.4408, 0.0767141]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.887812 -0.0239376 -0.0470626
0.0368741 0.875266 -0.0803964
0.0264707 0.0218503 0.733296
Offset = [-1.94789, 1.32478, 0.576526]
Background level guess :
first place: 0 (99.6543%)
second place: 214 (0.00496032%)
Guessed background level: 0
[AtlasCreator 14:32:59] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:33:00] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:33:00] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG17.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG17.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG17.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
373 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 246
LowHigh Thresholds: [0,90.8516,246]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2104750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 -0.00818715
-0.052336 0.986335 -0.15622
8.67362e-19 0.156434 0.987688
Offset: [5.17131, 2.74384, 11.8777]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [5.40075, -0.239463, 12.8021]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0516916 0.986335 0.156434
-0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, -0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998674 0.0507988 0.00838654
-0.0493561 0.990936 -0.124939
-0.0146573 0.12436 0.992129
Offset = [4.25874, 2.69743, 13.2042]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 67 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.958853 0.0476643 -0.0172573
-0.0494613 0.979255 -0.125797
0.0111029 0.126488 0.90761
Offset = [4.64191, 2.93081, 14.8903]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.941021 0.0395027 0.00722857
-0.0234727 0.966898 -0.165944
-0.0497583 0.129459 0.831414
Offset = [4.29868, 3.82079, 16.1556]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.936564 0.0503952 -0.0144109
-0.0424117 0.954913 -0.169219
-0.0434606 0.128031 0.810879
Offset = [4.5901, 3.28142, 16.6946]
Guessed background level: 0
[AtlasCreator 14:36:58] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:36:59] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:36:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
280 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 201
LowHigh Thresholds: [0,73.75,201]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x110e750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.987688 0.154508 0.0244717
-0.156434 0.975528 0.154508
1.73472e-18 -0.156434 0.987688
Offset: [3.53688, -3.42132, -3.70065]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [5.17201, -0.359738, -5.09483]
Inverse:
0.987688 -0.156434 1.73472e-18
0.154508 0.975528 -0.156434
0.0244717 0.154508 0.987688
Singular: 0
Versor: [ -0.0782172, 0.00615583, -0.0782172, 0.993844 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.991687 0.127827 -0.0147504
-0.123735 0.978786 0.163302
0.0353118 -0.160119 0.986466
Offset = [4.43347, -3.33769, -3.48575]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.977179 0.121889 -0.0537268
-0.113058 0.91991 0.144592
0.0704383 -0.13723 0.845023
Offset = [4.93264, -2.70674, -0.049308]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.965134 0.105599 -0.0689635
-0.0446415 0.922563 0.0859704
0.0559911 -0.138203 0.820617
Offset = [4.93263, -1.4317, 0.836949]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.972991 0.0957157 -0.0658135
-0.0334888 0.922192 0.085471
0.0514951 -0.140566 0.823002
Offset = [5.1697, -1.64134, 0.695874]
Guessed background level: 0
[AtlasCreator 14:40:49] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:40:50] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:40:50] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
266 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2812,177]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xddc750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 -0.0108813
0.052336 0.976807 0.207627
8.67362e-19 -0.207912 0.978148
Offset: [2.67115, -3.48725, -2.26238]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [2.08675, 0.203757, -4.22007]
Inverse:
0.99863 0.052336 8.67362e-19
-0.0511923 0.976807 -0.207912
-0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, -0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999798 -0.00686929 -0.0188882
0.00979356 0.987168 0.159382
0.017551 -0.159535 0.987036
Offset = [2.2657, -2.18171, -1.88547]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 235 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.971586 -0.00876968 -0.0517668
0.0176731 0.933222 0.174135
0.0494406 -0.17481 0.809404
Offset = [2.81761, -1.85346, 2.28765]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.956653 -0.022472 -0.0125209
0.0100334 0.923685 0.0908986
-0.00351533 -0.178406 0.781897
Offset = [1.58123, -0.609876, 2.9701]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.95745 -0.0209169 -0.0225448
0.00542293 0.930404 0.0937342
-0.00184038 -0.186766 0.789413
Offset = [2.22352, -0.821312, 3.03329]
Background level guess :
first place: 0 (99.81%)
second place: 65 (0.00279018%)
Guessed background level: 0
[AtlasCreator 14:45:38] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:45:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:45:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
294 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,69.1875,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xaf2750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 1.45062e-18
1.38778e-17 0.994522 -0.104528
0 0.104528 0.994522
Offset: [4.13147, 3.17272, 13.1802]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [4.13147, 1.13771, 13.8503]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 0.104528
1.45062e-18 -0.104528 0.994522
Singular: 0
Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999613 -0.0253191 -0.0115628
0.0249274 0.999149 -0.0328493
0.0123847 0.0325483 0.999393
Offset = [4.61472, 1.47583, 14.2998]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.959532 -0.0193229 -0.0214473
0.0184518 0.985611 -0.0400949
0.0222012 0.0396825 0.929581
Offset = [4.67264, 1.62747, 15.6198]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 80 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921066 -0.0344296 -0.0330066
0.0557911 0.95377 -0.0549332
-0.00212228 0.0421176 0.803778
Offset = [4.23447, 2.77044, 18.7608]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.929268 -0.029628 -0.0261079
0.0640485 0.953594 -0.0565938
0.00404999 0.0430441 0.791619
Offset = [4.21334, 2.48597, 19.2016]
Background level guess :
first place: 0 (99.9727%)
second place: 101 (0.0016276%)
Guessed background level: 0
[AtlasCreator 14:49:37] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:49:38] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:49:38] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 227
LowHigh Thresholds: [0,84.7656,227]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x218b750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.987688 -0.15622 -0.00818715
0.156434 0.986335 0.0516916
8.67362e-19 -0.052336 0.99863
Offset: [-1.12116, 1.87689, 7.43984]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-2.41185, 2.467, 7.02585]
Inverse:
0.987688 0.156434 8.67362e-19
-0.15622 0.986335 -0.052336
-0.00818715 0.0516916 0.99863
Singular: 0
Versor: [ -0.0260963, -0.00205382, 0.0784322, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.990641 -0.134326 0.0242085
0.132721 0.989406 0.0588382
-0.0318555 -0.0550746 0.997974
Offset = [-2.49702, 2.19667, 7.77152]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 92 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.922535 -0.131509 0.045652
0.129311 0.942461 0.048158
-0.0515485 -0.0417858 0.8707
Offset = [-3.21358, 2.82456, 10.631]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.917836 -0.141366 0.0374723
0.122088 0.935555 0.00786516
-0.0753927 -0.0843403 0.853341
Offset = [-2.86464, 3.58198, 11.3366]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920178 -0.145806 0.0276937
0.121048 0.925858 -0.014411
-0.0526472 -0.0733939 0.853102
Offset = [-2.5238, 3.7222, 11.5261]
Background level guess :
first place: 0 (99.8485%)
second place: 76 (0.00217014%)
Guessed background level: 0
[AtlasCreator 14:53:41] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:53:42] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:53:42] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG4.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG4.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG4.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 205
LowHigh Thresholds: [0,75.9375,205]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x230d750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [1.28398, 1.06793, 15.9937]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [1.28398, -2.00809, 16.9181]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999957 0.00803457 -0.00464967
-0.00869651 0.98601 -0.166457
0.00324721 0.16649 0.986038
Offset = [1.30883, 1.0569, 16.1399]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.918118 0.0241671 -0.0291617
-0.0279744 0.996041 -0.138142
0.0255321 0.138859 0.938446
Offset = [1.63031, 0.534382, 17.6377]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.844925 0.00981554 -0.0272847
-0.00753397 0.952316 -0.152713
0.0272113 0.121685 0.727775
Offset = [0.612485, 1.30821, 23.2808]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.83939 0.0092395 -0.0306225
-0.0034705 0.950869 -0.146314
0.0272979 0.116908 0.726119
Offset = [0.759706, 0.86679, 23.3666]
Background level guess :
first place: 0 (99.959%)
second place: 76 (0.00139509%)
Guessed background level: 0
[AtlasCreator 14:57:31] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 14:57:32] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 14:57:32] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,82.5,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2843750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [3.97799, 5.33546, 3.35903]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [3.75372, 2.15484, 4.2834]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999214 -0.0394393 0.00390029
0.0396006 0.989688 -0.13766
0.00156914 0.137706 0.990472
Offset = [3.57671, 4.69258, 4.21121]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.956556 -0.00641871 0.0187396
0.0084491 0.935296 -0.110363
-0.0179161 0.1105 0.836284
Offset = [2.73957, 5.07035, 7.69056]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93388 -0.0145722 -7.81718e-05
0.0199415 0.913926 -0.118159
-0.018693 0.0965702 0.780982
Offset = [3.49678, 5.37315, 8.52368]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.937597 -0.0140481 0.00456669
0.0143529 0.915769 -0.137358
-0.0235615 0.115754 0.767124
Offset = [3.2603, 5.39997, 8.87102]
Background level guess :
first place: 0 (99.998%)
second place: 84 (0.00031002%)
Guessed background level: 0
[AtlasCreator 15:01:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 15:01:30] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:01:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG6.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG6.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG6.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
286 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 209
LowHigh Thresholds: [0,77.25,209]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1284750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 -0.0108813
0.052336 0.976807 0.207627
8.67362e-19 -0.207912 0.978148
Offset: [1.39711, 0.979588, -0.550538]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [0.812716, 4.67059, -2.50823]
Inverse:
0.99863 0.052336 8.67362e-19
-0.0511923 0.976807 -0.207912
-0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, -0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 75 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999178 -0.0396322 0.00851834
0.0363803 0.969386 0.24283
-0.0178814 -0.24232 0.970032
Offset = [0.31274, -0.229117, 0.799176]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.875208 -0.036909 -0.0222076
0.0414344 0.90753 0.261238
0.0117747 -0.261916 0.814312
Offset = [0.703466, 0.780549, 3.77701]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.866196 -0.039407 -0.0232042
0.0324968 0.900227 0.207093
-0.00859325 -0.263272 0.800527
Offset = [0.545237, 1.84465, 4.25813]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 67 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.856296 -0.0459951 -0.0148812
0.0380676 0.901512 0.163521
-0.0227645 -0.230616 0.796463
Offset = [0.896292, 2.48913, 5.01403]
Background level guess :
first place: 0 (99.9101%)
second place: 51 (0.00201513%)
Guessed background level: 0
[AtlasCreator 15:05:39] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 15:05:40] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:05:40] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG7.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG7.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG7.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
285 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 210
LowHigh Thresholds: [0,77.5625,210]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x152d750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [0.548726, 2.64992, 14.878]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [0.269973, 0.508881, 15.5481]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998998 -0.0191243 -0.0404722
0.0150962 0.995112 -0.0975923
0.0421407 0.0968835 0.994403
Offset = [0.846563, 2.19428, 15.4694]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.925051 -0.00839021 -0.0335148
0.00579856 0.948058 -0.0766902
0.034059 0.0764501 0.858309
Offset = [0.658069, 2.02732, 18.3504]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.910046 -0.0056201 -0.0573507
-0.014451 0.935271 -0.107444
0.0300367 0.083896 0.788942
Offset = [0.882556, 2.69493, 20.296]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 79 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911189 -0.0101581 -0.0564606
-0.0082365 0.928209 -0.107891
0.0440801 0.0862063 0.775194
Offset = [0.950255, 2.61809, 20.8536]
Guessed background level: 0
[AtlasCreator 15:09:51] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 15:09:52] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:09:52] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
288 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,71.3672,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x113f750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.994522 0.104528 -1.45062e-18
-0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [0.305774, -0.536003, 9.67881]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [1.09072, -0.379548, 9.67881]
Inverse:
0.994522 -0.104528 0
0.104528 0.994522 1.38778e-17
-1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, -3.63154e-19, -0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996833 0.0794425 0.00355889
-0.0793981 0.99678 -0.0112498
-0.00444114 0.0109316 0.99993
Offset = [0.177296, 0.0174981, 9.65063]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.926301 0.0743403 -0.00656066
-0.0744595 0.970227 -0.0203305
0.00502972 0.0207623 0.944278
Offset = [0.112642, 0.293604, 11.255]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 96 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.885885 0.0558007 -0.0132386
-0.0234331 0.939491 -0.0599823
-0.00494942 0.0225921 0.848076
Offset = [0.138387, 1.35235, 13.2652]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 59 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.865793 0.0644877 -0.0138369
-0.0279323 0.917309 -0.0736044
-0.0199265 0.0124376 0.775308
Offset = [0.08288, 1.70785, 14.8355]
Guessed background level: 0
[AtlasCreator 15:14:07] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.9522%)
second place: 3 (0.00992063%)
Guessed background level: 0
[AtlasCreator 15:14:08] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:14:08] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG9.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG9.mat --outputVolume /var/tmp/haehn/Slicer3haehn/yP1NcjAtlasCreator/caseG9.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
305 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 198
LowHigh Thresholds: [0,70.8906,198]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
175 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 166
LowHigh Thresholds: [0,61.3406,166]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1a2e750)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-1.39398, -4.33087, 12.3709]
Center: [-1.88514, 7.41059, 19.0801]
Translation: [-0.804411, -0.442546, 10.4132]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 89 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996894 0.0493078 -0.0614125
-0.0377515 0.983514 0.176847
0.06912 -0.17398 0.98232
Offset = [-0.229395, -3.40828, 11.6327]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.937199 0.0205724 -0.0701862
-0.010694 0.898319 0.13832
0.0723531 -0.137199 0.887454
Offset = [0.184232, -1.68585, 13.8132]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.912955 0.010198 -0.0519273
0.0335246 0.879738 0.097655
0.0438246 -0.160028 0.81085
Offset = [-0.218743, -0.443476, 15.8328]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 55 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.903197 0.00198032 -0.0762914
0.0408667 0.873188 0.0657597
0.0496995 -0.143388 0.782161
Offset = [-0.0770752, 0.110645, 16.9102]
[AtlasCreator 15:18:16] Waiting for Registration to complete..
[AtlasCreator 15:18:21] DEBUG: All outputs exist!
[AtlasCreator 15:18:21] Starting iteration 2...
Warning: In /var/tmp/haehn/SLICER/TRUNK/Slicer3/Libs/MRML/vtkMRMLVolumeArchetypeStorageNode.cxx, line 478
vtkMRMLVolumeArchetypeStorageNode (0x7ffa09be3040): WriteData: removing old version of file /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Background level guess :
first place: 0 (99.6492%)
second place: 68 (0.00519283%)
Guessed background level: 0
[AtlasCreator 15:18:56] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:18:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:18:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
218 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 127
LowHigh Thresholds: [0,44.0234,127]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1256a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [-1.08419, 0.391231, -2.38823]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-0.799003, -1.43221, -1.72189]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998829 0.0479852 -0.00623392
-0.0483496 0.99487 -0.0888627
0.00193784 0.08906 0.996024
Offset = [-1.19962, 0.041265, -1.37323]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.963574 0.0532664 -0.0154871
-0.0539528 0.975189 -0.0479235
0.012894 0.0486852 0.800547
Offset = [-1.28148, -0.354518, 2.55415]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.961733 0.047452 -0.0266139
-0.0347384 0.982619 -0.0730973
0.0118003 0.0356525 0.798521
Offset = [-1.05769, -0.159639, 2.57154]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.96847 0.0455907 -0.0215787
-0.0373353 0.98119 -0.0734377
0.00663114 0.0431371 0.795492
Offset = [-1.20945, -0.177612, 2.4503]
Background level guess :
first place: 0 (99.8355%)
second place: 156 (0.00356523%)
Guessed background level: 0
[AtlasCreator 15:23:03] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:23:04] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:23:04] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
269 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,64.1875,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x17eca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4054
Debug: Off
Observers:
none
Matrix:
0.99863 0.0522642 0.00273905
-0.052336 0.997261 0.0522642
4.33681e-19 -0.052336 0.99863
Offset: [-1.06303, 0.0794182, -1.29306]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-0.63013, 1.07432, -1.6999]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0522642 0.997261 -0.052336
0.00273905 0.0522642 0.99863
Singular: 0
Versor: [ -0.026168, 0.000685233, -0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999404 0.0281135 0.0200092
-0.0287889 0.998997 0.0343059
-0.0190246 -0.0348615 0.999211
Offset = [-1.53282, 0.243074, -0.588982]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921459 0.0237381 0.0259806
-0.0241878 0.981861 0.0171316
-0.0255626 -0.0177494 0.808689
Offset = [-1.73633, 0.898208, 3.12204]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.917655 0.0140129 0.0161277
-0.02071 0.970916 -0.0203088
-0.0229437 -0.0446629 0.796884
Offset = [-1.45225, 1.5778, 3.50791]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.918003 0.0160448 0.0188026
-0.0259967 0.975195 -0.0203262
-0.0248877 -0.0413168 0.797419
Offset = [-1.65234, 1.20543, 3.47128]
Background level guess :
first place: 0 (99.1645%)
second place: 142 (0.0144934%)
Guessed background level: 0
[AtlasCreator 15:26:54] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:26:55] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:26:55] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
261 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 167
LowHigh Thresholds: [0,59.6953,167]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x10a3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.994522 -0.103956 0.0109262
0.104528 0.989074 -0.103956
1.73472e-18 0.104528 0.994522
Offset: [-1.90898, 1.2066, 1.03359]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-2.4653, -0.892659, 1.69993]
Inverse:
0.994522 0.104528 1.73472e-18
-0.103956 0.989074 0.104528
0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, 0.00273905, 0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 84 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.990481 -0.0827136 0.110023
0.0883385 0.994969 -0.0472647
-0.10556 0.0565341 0.992805
Offset = [-4.02391, 0.771316, 2.23849]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.917023 -0.086089 0.0945515
0.089342 0.974487 -0.0307207
-0.0914838 0.0389159 0.786999
Offset = [-3.85536, 0.175295, 5.85494]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.913939 -0.0975129 0.086778
0.137828 0.987515 -0.0419544
-0.110587 0.0243695 0.792876
Offset = [-3.70907, 0.430496, 5.6633]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920264 -0.0786479 0.0978317
0.122836 0.983391 -0.0490175
-0.110135 0.0290791 0.799533
Offset = [-3.9879, 0.758878, 5.70279]
Background level guess :
first place: 0 (99.9963%)
second place: 141 (0.00031002%)
Guessed background level: 0
[AtlasCreator 15:31:03] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:31:04] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:31:04] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
377 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.8906,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x13cda50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 -0.0163519
-0.104528 0.982278 -0.155578
0 0.156434 0.987688
Offset: [-1.66217, 3.16749, 4.14327]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.18994, 0.437689, 5.06728]
Inverse:
0.994522 -0.104528 0
0.103242 0.982278 0.156434
-0.0163519 -0.155578 0.987688
Singular: 0
Versor: [ 0.0783516, -0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998123 0.0566971 -0.0231427
-0.0584711 0.994665 -0.0849808
0.018201 0.0861745 0.996114
Offset = [-1.44679, 1.51256, 5.21694]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.914308 0.0624976 -0.0383193
-0.0648655 0.922418 -0.0640274
0.0341583 0.0663407 0.747943
Offset = [-1.4729, 1.93277, 9.95232]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.917641 0.053282 -0.043585
-0.0529421 0.917914 -0.0850372
0.0322714 0.0569198 0.7462
Offset = [-1.25134, 2.28209, 9.76299]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915125 0.0569046 -0.0456261
-0.0561118 0.915273 -0.0865819
0.0353854 0.0709704 0.751517
Offset = [-1.36219, 2.33163, 9.84272]
Guessed background level: 0
[AtlasCreator 15:34:55] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:34:56] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:34:56] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case19.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case19.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case19.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
331 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 220
LowHigh Thresholds: [0,81.1562,220]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x149ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0522642 -0.00273905
-0.052336 0.997261 -0.0522642
-6.50521e-19 0.052336 0.99863
Offset: [5.46602, 4.31964, 0.460965]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [5.8014, 3.45393, 0.819019]
Inverse:
0.99863 -0.052336 -6.50521e-19
0.0522642 0.997261 0.052336
-0.00273905 -0.0522642 0.99863
Singular: 0
Versor: [ 0.026168, -0.000685233, -0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998131 0.0602339 0.010281
-0.0605319 0.997664 0.0316677
-0.00834951 -0.0322309 0.999446
Offset = [5.20055, 2.63021, 1.58864]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.903154 0.0524776 0.0024402
-0.0524735 0.900263 -0.00171745
-0.00252696 0.00158704 0.77808
Offset = [5.01828, 4.13001, 5.51626]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905548 0.0476894 0.00182013
-0.0416576 0.89094 -0.0261815
-0.00656812 -0.00321981 0.773434
Offset = [4.97672, 4.3448, 5.78227]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.899099 0.0535076 -0.000625714
-0.051192 0.88999 -0.0297278
-0.00784025 -0.00393975 0.772217
Offset = [4.92411, 4.35446, 5.64902]
Background level guess :
first place: 0 (99.9893%)
second place: 41 (0.00031002%)
Guessed background level: 0
[AtlasCreator 15:38:47] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:38:48] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:38:48] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
245 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 157
LowHigh Thresholds: [0,57.2812,157]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2814a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.987688 0.15622 -0.00818715
-0.156434 0.986335 -0.0516916
0 0.052336 0.99863
Offset: [-0.879108, -4.82953, -8.87381]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [0.136653, -5.59659, -8.51575]
Inverse:
0.987688 -0.156434 0
0.15622 0.986335 0.052336
-0.00818715 -0.0516916 0.99863
Singular: 0
Versor: [ 0.0260963, -0.00205382, -0.0784322, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997347 0.0500626 -0.0528493
-0.0489048 0.998539 0.0229782
0.0539225 -0.0203327 0.998338
Offset = [0.194536, -5.89883, -7.25518]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.934822 0.0476203 -0.0631436
-0.0460512 0.903461 0.0260778
0.064297 -0.0230882 0.768772
Offset = [0.202704, -4.97849, -2.70789]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932686 0.044343 -0.0733474
-0.0679503 0.893449 -0.0231472
0.0458839 -0.0490274 0.76113
Offset = [0.376133, -4.51518, -2.76986]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.931315 0.0462014 -0.0686712
-0.0800875 0.896949 -0.0288431
0.0482987 -0.0475261 0.762124
Offset = [0.252524, -4.27557, -2.9056]
Background level guess :
first place: 0 (99.9754%)
second place: 87 (0.000697545%)
Guessed background level: 0
[AtlasCreator 15:42:37] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:42:38] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:42:38] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case20.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case20.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case20.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
274 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,64.5469,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x14e3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 -1.45062e-18
1.38778e-17 0.994522 0.104528
0 -0.104528 0.994522
Offset: [-1.1761, -1.05967, 8.68389]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.1761, 0.760919, 7.82253]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 -0.104528
-1.45062e-18 0.104528 0.994522
Singular: 0
Versor: [ -0.052336, -3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999467 0.00622011 -0.0320577
-0.0025325 0.993499 0.113811
0.0325572 -0.113669 0.992985
Offset = [-0.988838, -1.3407, 8.60948]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.973178 0.00705828 -0.0240679
-0.00525284 0.93575 0.0742692
0.0245253 -0.0741194 0.774484
Offset = [-1.16274, -0.350518, 13.1769]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.982241 0.0046996 -0.037231
0.0341433 0.93602 0.0556234
0.0258238 -0.0869532 0.774608
Offset = [-0.826328, 0.00104117, 13.2357]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.982582 0.0116271 -0.0241891
0.0379797 0.927396 0.0681964
0.0184785 -0.0901514 0.786052
Offset = [-1.06282, -0.0365083, 13.0601]
Guessed background level: 0
[AtlasCreator 15:46:30] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:46:31] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:46:31] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case23.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case23.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case23.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 181
LowHigh Thresholds: [0,64.5703,181]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x166da50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.27758, -0.63614, -4.55918]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [1.27758, 2.90502, -6.46748]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999645 0.0186593 -0.0190247
-0.0144738 0.979629 0.200296
0.0223745 -0.199949 0.979551
Offset = [1.18785, -0.418242, -3.86513]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 79 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.955817 0.00700616 -0.0350081
-0.00140699 0.901975 0.157468
0.0356745 -0.157318 0.757096
Offset = [1.63028, 0.902028, 0.22081]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.955043 0.00580735 -0.0321525
-0.00109644 0.898452 0.117163
0.0318736 -0.18795 0.731602
Offset = [1.47918, 1.51756, 0.63689]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.957776 0.00973472 -0.0333947
-0.000420755 0.903631 0.1079
0.0315604 -0.178221 0.731535
Offset = [1.56029, 1.44503, 0.515274]
Background level guess :
first place: 0 (99.606%)
second place: 143 (0.00759549%)
Guessed background level: 0
[AtlasCreator 15:50:33] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:50:34] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:50:34] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case26.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case26.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case26.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
259 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 171
LowHigh Thresholds: [0,61.1719,171]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1fd9a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104528 1.45062e-18
0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [-5.41886, -2.12979, -7.21555]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-6.17385, -2.33882, -7.21555]
Inverse:
0.994522 0.104528 0
-0.104528 0.994522 1.38778e-17
1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, 3.63154e-19, 0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 71 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99606 -0.0854867 0.0235706
0.0851364 0.996249 0.015486
-0.024806 -0.0134183 0.999602
Offset = [-6.44654, -1.98829, -6.71743]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.984137 -0.0870643 0.0146731
0.0868993 0.978847 0.0115289
-0.0156204 -0.0102087 0.828272
Offset = [-6.59508, -1.53649, -3.36099]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.982 -0.0777068 0.00237076
0.0871061 0.976748 -0.00668503
-0.0355827 -0.047962 0.805173
Offset = [-6.21275, -1.13244, -2.87258]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.983757 -0.0860731 0.00668956
0.0932896 0.977213 -0.0144824
-0.0384817 -0.0373404 0.811965
Offset = [-6.42226, -0.921354, -2.86173]
Background level guess :
first place: 0 (99.9778%)
second place: 228 (0.00093006%)
Guessed background level: 0
[AtlasCreator 15:54:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:54:30] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:54:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
340 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 240
LowHigh Thresholds: [0,89.9062,240]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1007a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104528 1.45062e-18
0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [-1.01673, 3.13307, -11.5879]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.77172, 2.92404, -11.5879]
Inverse:
0.994522 0.104528 0
-0.104528 0.994522 1.38778e-17
1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, 3.63154e-19, 0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997297 -0.0734106 0.0030333
0.0733564 0.99719 0.0152186
-0.00414198 -0.014955 0.99988
Offset = [-1.41569, 2.44271, -10.6351]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.881639 -0.0724897 0.00406354
0.0722774 0.909785 0.0389533
-0.00687354 -0.0385568 0.734158
Offset = [-2.08899, 3.01444, -6.42019]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.884676 -0.0653364 0.0024655
0.0514982 0.91538 0.0152086
-0.0202564 -0.0303645 0.733038
Offset = [-2.03766, 3.33345, -6.25573]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.88286 -0.0657951 0.00691955
0.0506569 0.907627 0.0224455
-0.023293 -0.0398719 0.727021
Offset = [-2.14091, 3.29481, -6.18594]
Guessed background level: 0
[AtlasCreator 15:58:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 15:58:26] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 15:58:26] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case29.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case29.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case29.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
228 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 172
LowHigh Thresholds: [0,62.9062,172]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x10c6a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-6.97207, 0.717234, -6.76805]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-6.40208, 4.32814, -8.67635]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997832 0.0467322 -0.0463426
-0.0371105 0.981037 0.190235
0.0543539 -0.188103 0.980644
Offset = [-5.87509, 1.07057, -6.62664]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 51 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.90627 0.0195441 -0.027839
-0.0152063 0.903293 0.14829
0.0304262 -0.147781 0.791451
Offset = [-6.34353, 2.74008, -3.29952]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902084 0.0118473 -0.0295268
-0.0695723 0.891729 0.071122
0.0389634 -0.174367 0.787108
Offset = [-6.5815, 3.61608, -3.11779]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.90668 0.0154178 -0.0268495
-0.076794 0.892817 0.0698702
0.0417956 -0.179097 0.781807
Offset = [-6.78938, 3.91146, -3.18263]
Background level guess :
first place: 0 (99.6932%)
second place: 135 (0.00364273%)
Guessed background level: 0
[AtlasCreator 16:02:32] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:02:33] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:02:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
324 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,69.3359,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xe38a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-5.83267, 3.91758, -2.46254]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-5.83267, 1.04307, -1.53853]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 66 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998933 -0.0325312 -0.0327914
0.0306082 0.997874 -0.057531
0.0345932 0.0564659 0.997805
Offset = [-5.11995, 1.26989, -1.44473]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907557 -0.0158215 -0.039424
0.014257 0.974484 -0.0396544
0.0400164 0.0390566 0.771796
Offset = [-5.30951, 1.06459, 3.48836]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.909281 -0.0210026 -0.0445548
0.0177014 0.970322 -0.0457063
0.0214068 0.0217974 0.761213
Offset = [-5.07804, 1.72817, 3.73281]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905812 -0.0203768 -0.0454667
0.0166242 0.973342 -0.0605541
0.0353205 0.0291935 0.769998
Offset = [-5.37466, 1.38781, 3.5091]
Background level guess :
first place: 0 (99.9661%)
second place: 125 (0.00100756%)
Guessed background level: 0
[AtlasCreator 16:06:32] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:06:34] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:06:34] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case32.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case32.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case32.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
253 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 162
LowHigh Thresholds: [0,58.4531,162]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x22cda50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [-2.15192, -2.62265, -9.79532]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-2.15192, 0.918511, -11.7036]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 161 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998945 -0.0345917 -0.0302141
0.0394602 0.983022 0.179192
0.0235026 -0.180196 0.98335
Offset = [-1.74919, -2.3263, -9.75552]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.90324 -0.0460827 -0.0675384
0.0573776 0.943259 0.176211
0.0582483 -0.179496 0.778417
Offset = [-1.15203, -1.90562, -5.803]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.892814 -0.040803 -0.0814928
0.0504646 0.93422 0.106332
0.0613692 -0.207594 0.757976
Offset = [-0.998425, -0.494728, -4.89519]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898952 -0.0363139 -0.0720419
0.0462234 0.943669 0.117129
0.0516943 -0.208812 0.763835
Offset = [-1.06809, -0.924204, -5.10648]
Guessed background level: 0
[AtlasCreator 16:11:01] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:11:02] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:11:02] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
224 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 144
LowHigh Thresholds: [0,52.8125,144]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2459a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [4.77519, -4.3892, -13.6094]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [5.30088, -1.62371, -14.9717]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997059 0.0625382 -0.0443026
-0.0556348 0.988182 0.142836
0.0527117 -0.139951 0.988754
Offset = [5.68014, -3.48281, -11.8799]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932675 0.0503911 -0.0395106
-0.044569 0.903343 0.13646
0.0459778 -0.134419 0.79286
Offset = [5.27433, -2.99525, -9.12853]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.927826 0.048008 -0.0520195
-0.0551876 0.90084 0.0599953
0.0438556 -0.165571 0.787879
Offset = [5.48934, -1.93063, -9.09899]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.92814 0.045975 -0.0530697
-0.0476972 0.898524 0.0565804
0.0429228 -0.161151 0.786782
Offset = [5.50338, -1.91928, -8.97926]
Background level guess :
first place: 0 (99.8568%)
second place: 144 (0.00224764%)
Guessed background level: 0
[AtlasCreator 16:14:59] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:15:01] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:15:01] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case36.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case36.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case36.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
273 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,63,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x26d9a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
0.978148 -0.207627 -0.0108813
0.207912 0.976807 0.0511923
8.67362e-19 -0.052336 0.99863
Offset: [-4.22012, -0.114405, -11.0949]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-5.89572, 0.291198, -11.5017]
Inverse:
0.978148 0.207912 8.67362e-19
-0.207627 0.976807 -0.052336
-0.0108813 0.0511923 0.99863
Singular: 0
Versor: [ -0.0260335, -0.00273624, 0.104493, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.983849 -0.163886 0.0719889
0.157931 0.984052 0.0818466
-0.0842543 -0.0691554 0.994042
Offset = [-6.15151, -1.03361, -10.0684]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908323 -0.157778 0.0503048
0.151837 0.962481 0.105647
-0.0661055 -0.0965504 0.778058
Offset = [-6.24747, -1.15594, -6.09678]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904407 -0.154691 0.0459136
0.125177 0.962249 0.060908
-0.0760617 -0.102517 0.772708
Offset = [-6.08087, -0.668381, -6.00582]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907007 -0.159615 0.0441068
0.124251 0.96594 0.0726456
-0.0827117 -0.108673 0.774186
Offset = [-6.07792, -0.909439, -6.09494]
Background level guess :
first place: 0 (99.9645%)
second place: 127 (0.000697545%)
Guessed background level: 0
[AtlasCreator 16:18:56] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:18:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:18:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case40.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case40.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case40.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 204
LowHigh Thresholds: [0,73.7344,204]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2043a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 0.0054706
-0.052336 0.993159 0.104385
-8.67362e-19 -0.104528 0.994522
Offset: [2.43044, -2.68202, -13.9458]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [2.91038, -0.78933, -14.8071]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0520493 0.993159 -0.104528
0.0054706 0.104385 0.994522
Singular: 0
Versor: [ -0.052318, 0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 79 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998753 0.0210364 -0.0452723
-0.0161884 0.99435 0.104906
0.0472234 -0.104042 0.993451
Offset = [3.12703, -2.1418, -12.8795]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.922271 0.0116913 -0.0555223
-0.00638516 0.93356 0.0948007
0.0563794 -0.0942935 0.86927
Offset = [3.30441, -1.41932, -10.6418]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.906088 0.0176283 -0.0446093
0.00394921 0.914743 0.0290781
0.0389198 -0.108208 0.771702
Offset = [2.95099, -0.508727, -8.85131]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911698 0.022984 -0.0513412
-0.00377899 0.922635 0.0325486
0.0348443 -0.106179 0.779833
Offset = [2.99212, -0.692427, -9.10665]
Background level guess :
first place: 0 (99.8872%)
second place: 69 (0.00271267%)
Guessed background level: 0
[AtlasCreator 16:23:00] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:23:02] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:23:02] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case41.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case41.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case41.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 139
LowHigh Thresholds: [0,50.0625,139]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e00a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 -1.45062e-18
1.38778e-17 0.994522 0.104528
0 -0.104528 0.994522
Offset: [-3.16562, -0.809088, -11.0583]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-3.16562, 1.0115, -11.9197]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 -0.104528
-1.45062e-18 0.104528 0.994522
Singular: 0
Versor: [ -0.052336, -3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999936 0.00365166 0.0106685
-0.00452006 0.996577 0.0825438
-0.0103305 -0.0825868 0.99653
Offset = [-3.46315, -0.703869, -11.6876]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911128 0.00190351 0.0368007
-0.00506388 0.958011 0.0859766
-0.0365003 -0.0861045 0.775496
Offset = [-4.34987, -0.181137, -6.38862]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.910895 0.00806935 0.0184395
-0.0299952 0.952707 0.0399036
-0.0485647 -0.104757 0.770949
Offset = [-3.89107, 0.265037, -6.65281]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.913386 -0.000961434 0.0156571
-0.0169994 0.941812 0.0401098
-0.0533817 -0.106257 0.769192
Offset = [-3.85711, 0.363138, -6.44695]
Guessed background level: 0
[AtlasCreator 16:26:52] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:26:53] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:26:53] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case42.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case42.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case42.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,70.1172,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x15d3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [-0.450207, -1.8591, -18.8006]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [0.0754806, 0.906384, -20.1629]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999332 -0.00682842 -0.0359
0.0126332 0.986371 0.164049
0.0342905 -0.164393 0.985799
Offset = [0.610649, -1.67175, -17.5409]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905917 -0.00635128 -0.0170896
0.00905061 0.934078 0.16284
0.0158266 -0.162967 0.753901
Offset = [-0.22942, -0.972593, -14.0605]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907769 0.00226044 -0.0297189
-0.0220026 0.927862 0.102621
0.00472743 -0.178608 0.757218
Offset = [0.122451, -0.124623, -14.2642]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907026 0.00298682 -0.0277722
-0.0229091 0.927702 0.100107
0.00947198 -0.182404 0.7511
Offset = [0.0398668, -0.136566, -14.0597]
Background level guess :
first place: 0 (99.7911%)
second place: 120 (0.00356523%)
Guessed background level: 0
[AtlasCreator 16:30:44] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:30:46] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:30:46] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case46.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case46.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case46.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
226 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,54.4219,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xfa3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [4.8507, 3.48013, -2.11754]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [4.67251, -0.469741, -0.987186]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999585 -0.0223784 0.0181642
0.0254793 0.980684 -0.193931
-0.0134735 0.194313 0.980847
Offset = [4.37468, 2.75371, -1.84876]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 91 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928218 -0.0131104 0.0222284
0.0163961 0.940377 -0.154759
-0.0199287 0.155072 0.799938
Offset = [3.98092, 2.89962, 1.6476]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921669 -0.0121737 0.00998152
-0.0157697 0.944832 -0.154779
-0.0571307 0.155385 0.797694
Offset = [4.41958, 2.9949, 1.5972]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.925044 -0.016672 0.0102704
-0.0168926 0.945379 -0.162287
-0.0578121 0.164556 0.800904
Offset = [4.35003, 2.92845, 1.63443]
Guessed background level: 0
[AtlasCreator 16:34:56] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:34:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:34:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case47.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case47.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case47.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
287 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,63.25,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x269aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 1.45062e-18
1.38778e-17 0.994522 -0.104528
0 0.104528 0.994522
Offset: [-5.95198, -1.89859, -0.0211375]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-5.95198, -3.79924, 0.645199]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 0.104528
1.45062e-18 -0.104528 0.994522
Singular: 0
Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
1 0.000161486 0.000633846
-9.71914e-05 0.994972 -0.100154
-0.000646832 0.100154 0.994972
Offset = [-5.91132, -2.21892, 0.190761]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 51 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.922638 -0.0104326 0.014475
0.0113199 0.883404 -0.0626319
-0.0137922 0.0627858 0.789265
Offset = [-6.57933, -1.87753, 4.57426]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928864 -0.00314844 0.00229748
0.0338967 0.884891 -0.0580747
-0.0234836 0.0580481 0.784142
Offset = [-6.45073, -2.08232, 4.82258]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.931305 -0.0098158 -0.000375078
0.0383046 0.882989 -0.0652791
-0.0192362 0.0668344 0.785722
Offset = [-6.41141, -1.97923, 4.86402]
Guessed background level: 0
[AtlasCreator 16:38:58] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:38:59] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:38:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case48.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case48.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case48.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
205 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 133
LowHigh Thresholds: [0,47.8047,133]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x107ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.987688 0.155578 -0.0163519
-0.156434 0.982278 -0.103242
-3.46945e-18 0.104528 0.994522
Offset: [0.265449, 1.04135, -11.7757]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [1.13118, -0.672948, -11.1093]
Inverse:
0.987688 -0.156434 -3.46945e-18
0.155578 0.982278 0.104528
-0.0163519 -0.103242 0.994522
Singular: 0
Versor: [ 0.0521746, -0.00410623, -0.0783516, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.993818 0.105713 -0.0339323
-0.107022 0.993475 -0.0394086
0.0295449 0.0427965 0.998647
Offset = [0.946003, -0.91813, -11.2016]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.939186 0.0889348 -0.0344021
-0.0888994 0.913499 0.00256007
0.0344935 0.000509923 0.773543
Offset = [0.687772, -0.846917, -5.52566]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.944703 0.0790392 -0.0485582
-0.0474643 0.906067 -0.0757208
0.0362311 -0.0125788 0.763265
Offset = [1.03715, 0.926342, -5.53745]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.949332 0.0753766 -0.0483887
-0.0397935 0.909171 -0.0725643
0.0400841 -0.0147959 0.772372
Offset = [1.03767, 0.670523, -5.62586]
Background level guess :
first place: 0 (99.7032%)
second place: 148 (0.00596788%)
Guessed background level: 0
[AtlasCreator 16:42:54] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:42:55] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:42:55] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,63.2109,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1abfa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [1.27609, 1.97592, -17.4117]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [1.80178, 4.74141, -18.774]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998361 0.0403867 0.0405479
-0.0451875 0.991068 0.125468
-0.0351185 -0.127095 0.991269
Offset = [0.597735, 2.39526, -17.2288]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.958272 0.0355462 0.0399084
-0.0407724 0.975428 0.138873
-0.0345517 -0.140302 0.858165
Offset = [0.32385, 2.47568, -14.5945]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.957184 0.0351575 0.0217084
-0.0581582 0.96602 0.103126
-0.0453137 -0.16115 0.820403
Offset = [0.604094, 3.13661, -13.5388]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.957023 0.0360023 0.0248902
-0.0592499 0.976372 0.0991328
-0.0445314 -0.158638 0.830992
Offset = [0.745834, 3.06011, -14.1798]
Background level guess :
first place: 0 (99.5194%)
second place: 159 (0.00658792%)
Guessed background level: 0
[AtlasCreator 16:46:43] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:46:45] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:46:45] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case51.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case51.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case51.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
265 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 174
LowHigh Thresholds: [0,63.7031,174]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1cc1a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 -0.0108813
-0.052336 0.976807 -0.207627
8.67362e-19 0.207912 0.978148
Offset: [1.8138, 0.655511, 6.5749]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [1.99642, -3.12513, 7.70525]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0511923 0.976807 0.207912
-0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99893 0.0286976 0.0362656
-0.0225442 0.986868 -0.159949
-0.0403795 0.15896 0.986459
Offset = [0.820008, -0.556776, 7.971]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.901118 0.0259715 0.0217379
-0.0226169 0.958821 -0.142428
-0.0252097 0.141855 0.793854
Offset = [1.06179, -0.576237, 11.4593]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 7 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902165 0.0238845 0.0236946
-0.0295293 0.962786 -0.144994
-0.0365436 0.130918 0.794391
Offset = [0.939012, -0.541761, 11.4117]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902728 0.0292001 0.0210211
-0.0329695 0.963745 -0.148978
-0.0390198 0.135837 0.79133
Offset = [1.11214, -0.391347, 11.5448]
Background level guess :
first place: 0 (99.921%)
second place: 111 (0.00124008%)
Guessed background level: 0
[AtlasCreator 16:50:26] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:50:28] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:50:28] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case53.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case53.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case53.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 195
LowHigh Thresholds: [0,72.1875,195]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1c65a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 0.0522642 -0.00273905
-0.052336 0.997261 -0.0522642
-6.50521e-19 0.052336 0.99863
Offset: [1.47175, 1.23798, -7.29783]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [1.80713, 0.37227, -6.93978]
Inverse:
0.99863 -0.052336 -6.50521e-19
0.0522642 0.997261 0.052336
-0.00273905 -0.0522642 0.99863
Singular: 0
Versor: [ 0.026168, -0.000685233, -0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99968 0.0208816 -0.014278
-0.0212376 0.999456 -0.0252508
0.013743 0.025546 0.999579
Offset = [1.35219, 0.991687, -6.82516]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.949386 0.0322807 0.000272433
-0.0322491 0.955168 -0.0366089
-0.00145387 0.036581 0.813265
Offset = [1.01394, 1.63464, -3.04256]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.948189 0.0334157 -0.00617572
-0.0362987 0.948296 -0.0633467
-0.0171273 0.0157891 0.805256
Offset = [1.1015, 2.32159, -2.78876]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.944607 0.036118 -0.0130198
-0.0440945 0.946548 -0.0627411
-0.0152781 0.0177925 0.807321
Offset = [1.41286, 2.3578, -2.68602]
Guessed background level: 0
[AtlasCreator 16:54:17] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:54:18] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:54:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case54.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case54.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case54.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
295 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 196
LowHigh Thresholds: [0,73.4062,196]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xd95a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-3.43563, 1.24537, -2.82481]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-2.86564, 4.85628, -4.73311]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999777 0.00465887 0.0205795
-0.00808635 0.985453 0.169754
-0.0194892 -0.169883 0.985272
Offset = [-3.3497, 1.89144, -3.32771]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 75 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.894119 0.015477 0.0109588
-0.0165669 0.864673 0.107568
-0.00922887 -0.107731 0.7432
Offset = [-3.80179, 4.91385, 1.5012]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 47 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.893943 0.0139103 0.00185524
-0.0283152 0.853863 0.0440186
-0.016796 -0.122594 0.733283
Offset = [-3.45297, 5.28713, 1.49351]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.892505 0.0153294 -0.000109873
-0.0342439 0.856327 0.0487484
-0.0153201 -0.129716 0.732255
Offset = [-3.57045, 5.44723, 1.63111]
Background level guess :
first place: 0 (99.8487%)
second place: 86 (0.00263517%)
Guessed background level: 0
[AtlasCreator 16:58:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 16:58:27] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 16:58:27] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case57.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case57.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case57.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
264 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 169
LowHigh Thresholds: [0,60.8125,169]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xf0aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [-1.5596, 1.98077, -0.66848]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.78939, -0.984437, 0.255526]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999655 -0.0104468 0.0241071
0.0131131 0.993481 -0.113239
-0.022767 0.113516 0.993275
Offset = [-1.97431, 0.981589, -0.223521]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.936064 -0.0161813 0.0195747
0.0176054 0.930226 -0.0749141
-0.0183044 0.0752346 0.773345
Offset = [-2.5229, 1.14342, 3.97956]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.931952 -0.0167149 0.0143403
0.0195513 0.930842 -0.104044
-0.0297196 0.0644801 0.764705
Offset = [-2.26184, 1.60688, 4.02766]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.935502 -0.00932149 0.0154407
0.0111938 0.930545 -0.0933691
-0.0266561 0.0612059 0.771839
Offset = [-2.30778, 1.54966, 3.90432]
Guessed background level: 0
[AtlasCreator 17:02:22] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:02:23] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:02:23] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case59.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case59.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case59.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,70.0312,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x22ada50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [1.83545, 0.893477, -4.53006]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [2.12064, -0.929967, -3.86372]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999193 0.0401523 0.00067981
-0.0400025 0.99667 -0.0710538
-0.00353052 0.0709693 0.997472
Offset = [1.92721, 0.281846, -4.42862]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928983 0.0613003 0.0186714
-0.0603841 0.90481 -0.0462101
-0.0214501 0.0449877 0.782888
Offset = [0.995361, 0.366362, 1.14555]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924812 0.0541033 4.95527e-05
-0.0414066 0.906158 -0.0523557
-0.024866 0.0197205 0.776623
Offset = [1.27499, 0.435347, 0.972341]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.922695 0.0637433 0.00575033
-0.0508544 0.899577 -0.0602879
-0.0381349 0.0261522 0.77925
Offset = [1.22751, 0.668699, 0.76365]
Guessed background level: 0
[AtlasCreator 17:06:19] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:06:21] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:06:21] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case60.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case60.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case60.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
338 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 239
LowHigh Thresholds: [0,90.25,239]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x200aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 -2.17096e-18
1.38778e-17 0.987688 0.156434
-1.92593e-34 -0.156434 0.987688
Offset: [-1.62537, -1.82395, -0.500926]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.62537, 0.870627, -1.86323]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.37069e-17 0.987688 -0.156434
-2.17096e-18 0.156434 0.987688
Singular: 0
Versor: [ -0.0784591, -5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999192 0.0391661 -0.00904756
-0.0373116 0.987402 0.153771
0.0149562 -0.153309 0.988065
Offset = [-2.19715, -2.00204, -0.677646]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.895569 0.0297696 -0.0558625
-0.0265242 0.908303 0.0579656
0.0574745 -0.0563676 0.732141
Offset = [-1.32806, 0.736398, 4.1675]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.892195 0.0309915 -0.0650454
-0.0304946 0.903077 -0.00188962
0.0516794 -0.0682094 0.72736
Offset = [-1.36158, 1.59108, 4.23515]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.890416 0.0355893 -0.0635165
-0.037407 0.902182 -0.000942597
0.0495249 -0.0698345 0.722489
Offset = [-1.34182, 1.65498, 4.33865]
Background level guess :
first place: 0 (99.929%)
second place: 112 (0.00186012%)
Guessed background level: 0
[AtlasCreator 17:10:09] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:10:10] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:10:10] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case61.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case61.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case61.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,53.9062,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xb5fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-1.25113, -0.654718, 3.85865]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.42932, -4.60459, 4.989]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997799 -0.0375856 0.0546287
0.0497048 0.969252 -0.240999
-0.0438909 0.243184 0.968987
Offset = [-2.37401, -0.45187, 4.25643]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.959612 -0.0241981 0.0672745
0.0399147 0.898659 -0.243195
-0.0593146 0.245258 0.776141
Offset = [-2.85407, -0.0253975, 7.64094]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 74 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.963064 -0.0199153 0.0460137
0.0561846 0.896606 -0.234544
-0.0663257 0.225517 0.771221
Offset = [-2.26729, 0.492681, 7.97511]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.962946 -0.0218684 0.0466627
0.0502844 0.901082 -0.245462
-0.0732811 0.2324 0.773647
Offset = [-2.29721, 0.431531, 7.83583]
Background level guess :
first place: 0 (99.9685%)
second place: 147 (0.000852555%)
Guessed background level: 0
[AtlasCreator 17:14:11] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:14:12] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:14:12] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case62.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case62.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case62.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
252 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,62.1562,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x13d7a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-3.43753, 7.22195, -1.9089]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-3.43753, 4.34744, -0.984894]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 83 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999574 -0.0280494 -0.00810799
0.0271797 0.995336 -0.0925634
0.0106665 0.0923036 0.995674
Offset = [-3.05443, 5.18423, -1.30815]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.931603 -0.0318471 -0.00442363
0.0319143 0.900024 0.0160605
0.00390933 -0.0161933 0.763841
Offset = [-3.54802, 4.04345, 4.72407]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.934795 -0.0296536 -0.0159265
0.0195232 0.889855 -0.0380388
-0.012371 -0.0337097 0.759285
Offset = [-3.43609, 5.53808, 4.61008]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932885 -0.0251545 -0.0120431
0.019048 0.892897 -0.0447258
-0.0158506 -0.0297778 0.749809
Offset = [-3.46434, 5.40051, 4.75733]
Background level guess :
first place: 0 (99.5161%)
second place: 137 (0.00713046%)
Guessed background level: 0
[AtlasCreator 17:18:13] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:18:15] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:18:15] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/case8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
263 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 160
LowHigh Thresholds: [0,58.2422,160]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1ab0a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [0.545672, -1.07284, 6.74757]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [0.264912, -3.06552, 7.41391]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999763 -0.021621 -0.00260409
0.0213801 0.997221 -0.0713718
0.00413998 0.0712992 0.997446
Offset = [0.435979, -1.62422, 8.14445]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.848081 -0.034571 -0.0280046
0.0333178 0.977654 -0.0440446
0.0294846 0.0430679 0.76672
Offset = [0.210772, -1.30224, 11.6937]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.851036 -0.0338136 -0.0392472
0.0127565 0.980741 -0.0681337
0.00546584 0.0328335 0.764188
Offset = [0.712933, -1.09497, 11.6807]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.854499 -0.029724 -0.0270407
0.00815029 0.97761 -0.0637471
0.00293319 0.0288587 0.766683
Offset = [0.314634, -1.1566, 11.6719]
Background level guess :
first place: 0 (99.7564%)
second place: 38 (0.00302269%)
Guessed background level: 0
[AtlasCreator 17:22:13] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:22:15] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:22:15] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG1.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG1.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG1.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
347 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 234
LowHigh Thresholds: [0,86.4844,234]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1520a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 0.104385 -0.0054706
-0.104528 0.993159 -0.0520493
4.33681e-19 0.052336 0.99863
Offset: [0.902939, -1.83826, 4.41093]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [1.57722, -2.64574, 4.76899]
Inverse:
0.994522 -0.104528 4.33681e-19
0.104385 0.993159 0.052336
-0.0054706 -0.0520493 0.99863
Singular: 0
Versor: [ 0.0261411, -0.00137, -0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.994534 0.0611723 -0.0846143
-0.0601261 0.99808 0.0148601
0.0853609 -0.00969138 0.996303
Offset = [2.83616, -2.32307, 4.66712]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.910937 0.0501054 -0.0833876
-0.0503547 0.959203 -0.000887198
0.0832373 0.00508194 0.811662
Offset = [2.13326, -1.7723, 8.97181]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.912876 0.0452098 -0.0839695
-0.0144903 0.963883 0.00100292
0.0708545 0.00669357 0.808021
Offset = [2.44717, -1.76365, 8.93129]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907761 0.0487995 -0.0797931
-0.0243656 0.959086 -9.62034e-05
0.0776359 0.00638259 0.809966
Offset = [2.1968, -1.54622, 8.9541]
Background level guess :
first place: 0 (99.7627%)
second place: 186 (0.00410776%)
Guessed background level: 0
[AtlasCreator 17:26:07] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:26:09] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:26:09] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 215
LowHigh Thresholds: [0,80.8828,215]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x24bba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [3.62569, 2.63404, 15.6182]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [3.34493, 0.641365, 16.2845]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 89 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997587 -0.0665608 -0.0197512
0.0650163 0.995384 -0.0705882
0.0243585 0.0691337 0.99731
Offset = [3.87962, 1.99861, 17.0221]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902182 -0.0544123 -0.0176785
0.052845 0.953034 -0.0794978
0.0219234 0.0784334 0.785327
Offset = [3.39692, 2.33451, 20.7762]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.906925 -0.0580658 -0.0232113
0.0522191 0.944587 -0.122213
-0.00305369 0.0546633 0.779775
Offset = [3.63794, 3.13507, 20.8119]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905054 -0.0601931 -0.0292843
0.0456121 0.944823 -0.122148
0.0049468 0.0498257 0.771391
Offset = [3.71954, 3.38378, 20.8914]
Background level guess :
first place: 0 (99.8225%)
second place: 6 (0.00767299%)
Guessed background level: 0
[AtlasCreator 17:30:07] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:30:09] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:30:09] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG11.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG11.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG11.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.7344,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x15d0a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 1.45062e-18
1.38778e-17 0.994522 -0.104528
0 0.104528 0.994522
Offset: [3.51707, -0.597443, 8.58839]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [3.51707, -2.49809, 9.25473]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 0.104528
1.45062e-18 -0.104528 0.994522
Singular: 0
Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 47 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999497 0.0194144 0.0250884
-0.017538 0.997181 -0.072962
-0.0264342 0.0724853 0.997019
Offset = [3.03848, -0.854996, 10.2479]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89965 0.0123109 0.0266273
-0.0112126 0.937909 -0.0410107
-0.0271081 0.0406945 0.787123
Offset = [2.37998, -0.873661, 13.0822]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.895066 0.0104429 0.0152966
-0.00220081 0.934569 -0.0766315
-0.0492432 0.0422601 0.778353
Offset = [2.58262, -0.441418, 13.1687]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89752 0.0130301 0.00969966
-0.0231349 0.929893 -0.0751701
-0.0503743 0.0394913 0.779121
Offset = [2.6912, -0.438551, 13.3374]
Guessed background level: 0
[AtlasCreator 17:34:07] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:34:08] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:34:08] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
321 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.5,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1294a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-1.32304, 2.34884, -0.102893]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.32304, -0.525677, 0.821112]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999892 -0.013631 -0.00549912
0.0128727 0.992688 -0.120018
0.00709488 0.119935 0.992756
Offset = [-0.663016, 1.25971, 0.0318383]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.87427 -0.00457293 0.0251802
0.00479254 0.893815 -0.00866777
-0.0251394 0.00878561 0.737036
Offset = [-2.15256, 0.502371, 6.83031]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.874108 -0.0071682 0.0111363
-0.01123 0.892755 -0.0546044
-0.04912 -0.00521316 0.735812
Offset = [-1.90961, 1.40461, 6.40337]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.87338 -0.00533069 0.00877317
-0.0208437 0.889854 -0.0573437
-0.054227 -0.00790395 0.739786
Offset = [-1.92553, 1.45416, 6.27051]
Background level guess :
first place: 0 (99.7555%)
second place: 81 (0.00325521%)
Guessed background level: 0
[AtlasCreator 17:37:53] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:37:54] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:37:54] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG13.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG13.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG13.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.0938,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xdfba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0522642 0.00273905
0.052336 0.997261 -0.0522642
4.33681e-19 0.052336 0.99863
Offset: [-0.908415, -0.0447671, 11.3594]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.23937, -1.0797, 11.7174]
Inverse:
0.99863 0.052336 4.33681e-19
-0.0522642 0.997261 0.052336
0.00273905 -0.0522642 0.99863
Singular: 0
Versor: [ 0.026168, 0.000685233, 0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998256 -0.036611 0.0463012
0.0379851 0.998853 -0.0291541
-0.0451808 0.030862 0.998502
Offset = [-1.51711, -0.88566, 12.2045]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.939715 -0.0170753 0.0450226
0.0186792 0.956738 -0.0354468
-0.0443811 0.0362467 0.798137
Offset = [-2.1323, -0.226078, 15.8758]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.941351 -0.020007 0.039377
0.0326017 0.952271 -0.0697718
-0.0610194 0.0257439 0.786921
Offset = [-2.11723, 0.318745, 16.1456]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.941808 -0.0185761 0.0391928
0.0326824 0.956134 -0.0608251
-0.0665556 0.0317343 0.801622
Offset = [-1.82509, -0.00625262, 15.8169]
Background level guess :
first place: 0 (98.828%)
second place: 187 (0.0134859%)
Guessed background level: 0
[AtlasCreator 17:41:49] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:41:51] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:41:51] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
348 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,80.2812,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x15d1a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.20562, 3.24148, 12.335]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [3.20562, -0.619058, 13.4654]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999929 0.00233414 0.0116478
0.000235977 0.97641 -0.215925
-0.011877 0.215912 0.976341
Offset = [2.74463, 3.01821, 13.7532]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.944391 0.00100289 0.00468277
-8.54187e-05 0.972083 -0.191943
-0.00478819 0.191941 0.844073
Offset = [2.49086, 2.40803, 16.282]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.94179 -0.00483436 0.000747567
0.0175308 0.975781 -0.199149
-0.0403269 0.204707 0.830922
Offset = [2.82498, 2.59945, 16.5944]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.949243 0.000197491 -0.0012005
0.0152124 0.979955 -0.19556
-0.0490067 0.20165 0.845346
Offset = [2.93478, 2.57113, 16.1201]
Background level guess :
first place: 0 (99.838%)
second place: 81 (0.00387525%)
Guessed background level: 0
[AtlasCreator 17:45:37] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:45:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:45:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 186
LowHigh Thresholds: [0,69.8438,186]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1ca1a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 -0.00818715
0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [0.749942, -4.24437, -3.28345]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [0.228686, -1.64811, -4.64575]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 -0.156434
-0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, -0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 60 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998392 -0.0516455 -0.0233596
0.0545133 0.987775 0.146041
0.0155317 -0.147079 0.989003
Offset = [0.816983, -3.28243, -2.74565]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.937641 -0.0479734 -0.0213891
0.0502267 0.950933 0.121605
0.0153693 -0.122512 0.825315
Offset = [0.671852, -2.63268, 0.523509]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.938565 -0.0458041 -0.0260088
0.110511 0.94355 0.0411056
0.00920162 -0.139178 0.812169
Offset = [0.726177, -1.42648, 0.821972]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.938319 -0.0361379 -0.0243439
0.0985711 0.944686 0.0369923
0.0126407 -0.139101 0.81349
Offset = [0.607585, -1.52659, 0.803718]
Guessed background level: 0
[AtlasCreator 17:49:47] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:49:48] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:49:48] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG16.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG16.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG16.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 225
LowHigh Thresholds: [0,84.6094,225]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1f5ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-1.71626, 3.32863, -5.59692]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.89444, -0.621243, -4.46657]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.9991 -0.0368116 -0.021056
0.0337346 0.990754 -0.131411
0.0256988 0.130583 0.991104
Offset = [-1.57819, 1.4399, -4.89407]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.871978 -0.0243139 -0.0322318
0.0233711 0.872568 -0.0293139
0.0329219 0.0285367 0.728924
Offset = [-1.65311, 0.824407, 1.51186]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.87954 -0.0222958 -0.0425082
0.0417967 0.871874 -0.0864518
0.0200607 0.0161641 0.72744
Offset = [-1.60908, 1.60901, 1.25617]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.881837 -0.0250488 -0.0430665
0.0418538 0.875596 -0.082959
0.0194717 0.0231159 0.730548
Offset = [-1.60896, 1.55346, 0.88212]
Background level guess :
first place: 0 (99.6543%)
second place: 214 (0.00496032%)
Guessed background level: 0
[AtlasCreator 17:53:38] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:53:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:53:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG17.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG17.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG17.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
373 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 246
LowHigh Thresholds: [0,90.8516,246]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xd4ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 -0.00818715
-0.052336 0.986335 -0.15622
8.67362e-19 0.156434 0.987688
Offset: [4.89813, 2.65954, 13.1581]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [5.13236, -0.136432, 14.0821]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0516916 0.986335 0.156434
-0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, -0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999243 0.037917 0.00872586
-0.0362796 0.989036 -0.143151
-0.0140581 0.142726 0.989662
Offset = [4.31437, 2.74121, 14.0031]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924483 0.0503991 0.0111423
-0.0485026 0.954622 -0.131409
-0.0176553 0.130693 0.79129
Offset = [4.04137, 3.04774, 17.761]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920469 0.0489958 -0.00381575
-0.0398753 0.953035 -0.163415
-0.0473372 0.11634 0.784114
Offset = [4.33806, 3.63093, 17.5457]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 68 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.919468 0.046719 -0.00821906
-0.0390288 0.950757 -0.167754
-0.0468213 0.122872 0.788316
Offset = [4.35787, 3.77354, 17.6231]
Guessed background level: 0
[AtlasCreator 17:57:40] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 17:57:41] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 17:57:41] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
280 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 201
LowHigh Thresholds: [0,73.75,201]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1aa4a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 0.0163519
-0.104528 0.982278 0.155578
1.73472e-18 -0.156434 0.987688
Offset: [3.84925, -3.06549, -2.45253]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [4.90362, -0.256707, -3.81483]
Inverse:
0.994522 -0.104528 1.73472e-18
0.103242 0.982278 -0.156434
0.0163519 0.155578 0.987688
Singular: 0
Versor: [ -0.0783516, 0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.994144 0.0963896 -0.048859
-0.0890908 0.98693 0.134281
0.0611637 -0.129141 0.989738
Offset = [4.58662, -2.75206, -2.37916]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.947531 0.0749211 -0.0690867
-0.0662209 0.903946 0.120607
0.0774657 -0.115404 0.807034
Offset = [4.94845, -2.12248, 1.87545]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.949674 0.0901464 -0.074188
-0.0294201 0.904405 0.0864904
0.05921 -0.146521 0.797841
Offset = [5.14092, -1.48738, 1.89756]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.95127 0.0870742 -0.0751664
-0.0192121 0.903426 0.0784097
0.0579339 -0.138121 0.799592
Offset = [5.16674, -1.25405, 1.92037]
Guessed background level: 0
[AtlasCreator 18:01:37] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:01:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:01:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
266 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2812,177]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x25baa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.81836, -3.23437, -1.03177]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [1.81836, 0.306787, -2.94007]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999945 -0.00414307 0.00965823
0.00236415 0.984137 0.177396
-0.01024 -0.177363 0.984092
Offset = [1.50555, -2.75226, -1.28671]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.947713 -0.00148606 -0.00734695
0.0025508 0.91005 0.147115
0.00704837 -0.147129 0.786974
Offset = [1.54776, -1.24916, 2.92564]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.953956 -0.00500872 -0.0129637
0.000164884 0.916218 0.0842799
-0.00139718 -0.17271 0.777609
Offset = [1.93861, -0.768889, 2.82973]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.949298 -0.00907413 -0.0140416
-0.00111691 0.916152 0.0877987
-0.00793895 -0.180422 0.777693
Offset = [2.00859, -0.961127, 2.83877]
Background level guess :
first place: 0 (99.81%)
second place: 65 (0.00279018%)
Guessed background level: 0
[AtlasCreator 18:05:36] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:05:38] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:05:38] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
294 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,69.1875,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x101da50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0522642 0.00273905
0.052336 0.997261 -0.0522642
4.33681e-19 0.052336 0.99863
Offset: [4.19403, 2.27568, 14.7722]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [3.86308, 1.24074, 15.1303]
Inverse:
0.99863 0.052336 4.33681e-19
-0.0522642 0.997261 0.052336
0.00273905 -0.0522642 0.99863
Singular: 0
Versor: [ 0.026168, 0.000685233, 0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998825 -0.0481546 0.00545263
0.0484133 0.996537 -0.0675998
-0.00217851 0.0677844 0.997698
Offset = [4.07467, 1.81766, 14.7157]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905092 -0.0337547 -0.00735161
0.0334807 0.936161 -0.0346542
0.00851281 0.0343874 0.782743
Offset = [4.0022, 2.26341, 19.0174]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908523 -0.0320362 -0.0201341
0.0620998 0.934415 -0.0411234
-0.0140092 0.0274689 0.773067
Offset = [4.31651, 2.50093, 19.238]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.909391 -0.0271299 -0.0224965
0.0633663 0.93157 -0.0519614
-0.0100137 0.0358131 0.771929
Offset = [4.28696, 2.62582, 19.3593]
Background level guess :
first place: 0 (99.9727%)
second place: 101 (0.0016276%)
Guessed background level: 0
[AtlasCreator 18:09:23] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:09:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:09:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 227
LowHigh Thresholds: [0,84.7656,227]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x27a6a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.987688 -0.15622 -0.00818715
0.156434 0.986335 0.0516916
8.67362e-19 -0.052336 0.99863
Offset: [-1.41283, 2.00269, 8.71269]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-2.68024, 2.57003, 8.30585]
Inverse:
0.987688 0.156434 8.67362e-19
-0.15622 0.986335 -0.052336
-0.00818715 0.0516916 0.99863
Singular: 0
Versor: [ -0.0260963, -0.00205382, 0.0784322, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.989729 -0.138621 0.0349465
0.136107 0.988478 0.0662304
-0.0437247 -0.0607937 0.997192
Offset = [-3.29549, 2.20234, 8.77669]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908157 -0.126043 0.0299559
0.124652 0.92282 0.0444643
-0.0352968 -0.0403555 0.830011
Offset = [-2.8583, 3.00474, 12.2341]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.906733 -0.127662 0.032091
0.0964659 0.919872 -0.0150957
-0.0656846 -0.0738237 0.815772
Offset = [-2.99198, 3.79209, 12.6024]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904748 -0.129188 0.0265937
0.10194 0.916756 -0.0200861
-0.0545985 -0.0646382 0.822443
Offset = [-2.84272, 3.75514, 12.5476]
Background level guess :
first place: 0 (99.8485%)
second place: 76 (0.00217014%)
Guessed background level: 0
[AtlasCreator 18:13:22] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:13:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:13:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG4.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG4.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG4.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 205
LowHigh Thresholds: [0,75.9375,205]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2129a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [1.24538, 1.06014, 17.2741]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [1.01559, -1.90506, 18.1981]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 47 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999529 -0.0151334 -0.0266876
0.0113733 0.99067 -0.135805
0.0284938 0.135437 0.990376
Offset = [1.25872, 0.58866, 17.8413]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 71 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.837042 -0.0010066 -0.0336251
-0.00283047 0.949901 -0.113871
0.0335208 0.113902 0.720065
Offset = [0.609983, 0.628057, 23.3418]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.842383 0.00021782 -0.0289966
0.00967623 0.941799 -0.139552
0.0306757 0.119822 0.72018
Offset = [0.68474, 0.980211, 23.3963]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.838075 -0.000470174 -0.0377395
0.00609877 0.947861 -0.1394
0.024985 0.117684 0.71854
Offset = [0.685762, 0.82192, 23.4149]
Background level guess :
first place: 0 (99.959%)
second place: 76 (0.00139509%)
Guessed background level: 0
[AtlasCreator 18:17:26] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:17:28] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:17:28] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,82.5,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2666a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.48532, 6.11841, 4.43304]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [3.48532, 2.25787, 5.56339]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 73 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999838 -0.0145726 0.0105678
0.0158938 0.990279 -0.138184
-0.00845143 0.138329 0.99035
Offset = [3.27644, 5.05318, 5.17147]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.927828 -0.0170442 0.00589367
0.0175993 0.901391 -0.112531
-0.00393732 0.112616 0.754957
Offset = [2.86206, 5.45647, 9.69521]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924667 -0.0215885 -0.00103066
0.0295851 0.894104 -0.145664
-0.0108155 0.101473 0.753207
Offset = [3.12533, 6.10514, 9.7933]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921158 -0.025903 -0.00483452
0.0266518 0.898603 -0.141891
-0.0122375 0.107683 0.759201
Offset = [3.13817, 5.79333, 9.76112]
Background level guess :
first place: 0 (99.998%)
second place: 84 (0.00031002%)
Guessed background level: 0
[AtlasCreator 18:21:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:21:30] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:21:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG6.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG6.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG6.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
286 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 209
LowHigh Thresholds: [0,77.25,209]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1f96a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 -0.0108813
0.052336 0.976807 0.207627
8.67362e-19 -0.207912 0.978148
Offset: [1.10989, 1.33194, 0.680068]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [0.544324, 4.77362, -1.22823]
Inverse:
0.99863 0.052336 8.67362e-19
-0.0511923 0.976807 -0.207912
-0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, -0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999052 -0.0423403 -0.0101343
0.0435295 0.967377 0.249575
-0.000763429 -0.24978 0.968302
Offset = [0.571892, 0.864031, 1.02967]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 93 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.852069 -0.0418267 -0.00311559
0.041431 0.892756 0.22859
-0.00653081 -0.228518 0.781571
Offset = [0.168686, 1.7439, 5.02055]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.845758 -0.0434748 -0.00465301
0.0271846 0.88875 0.176984
-0.0323922 -0.245659 0.770563
Offset = [0.493461, 2.30083, 5.29059]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.849094 -0.0397347 -0.0088349
0.0293679 0.893535 0.172098
-0.0284473 -0.24244 0.771824
Offset = [0.444173, 2.44452, 5.14082]
Background level guess :
first place: 0 (99.9101%)
second place: 51 (0.00201513%)
Guessed background level: 0
[AtlasCreator 18:25:35] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:25:37] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:25:37] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG7.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG7.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG7.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
285 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 210
LowHigh Thresholds: [0,77.5625,210]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x18c3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [0.231372, 3.57712, 15.9041]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [0.0015806, 0.611911, 16.8281]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999003 -0.0272738 -0.03533
0.0224696 0.991275 -0.129879
0.038564 0.128956 0.9909
Offset = [1.26929, 3.0778, 16.3776]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89378 -0.0274354 -0.0471857
0.0227928 0.918084 -0.0962585
0.0495952 0.0950395 0.770052
Offset = [0.414588, 2.60828, 21.263]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 9 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.896424 -0.024746 -0.0486858
0.0133553 0.916955 -0.107402
0.0372563 0.0835624 0.765624
Offset = [0.574957, 2.88119, 21.3123]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.899162 -0.0238036 -0.049774
0.0176458 0.919473 -0.113
0.0388313 0.083089 0.77086
Offset = [0.633878, 2.95242, 21.2079]
Guessed background level: 0
[AtlasCreator 18:29:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:29:30] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:29:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
288 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,71.3672,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x28aaa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.994522 0.103956 -0.0109262
-0.104528 0.989074 -0.103956
-8.67362e-19 0.104528 0.994522
Offset: [0.248293, 1.48475, 10.2925]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [0.822326, -0.276517, 10.9588]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.103956 0.989074 0.104528
-0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, -0.00273905, -0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996559 0.0827617 0.00449409
-0.0824002 0.995137 -0.0539737
-0.00893919 0.0534177 0.998532
Offset = [-0.0956372, 0.59722, 11.6329]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 63 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.848291 0.0676085 -0.00991281
-0.0679537 0.913398 -0.040052
0.00717406 0.040632 0.747535
Offset = [-0.488561, 0.502639, 17.5248]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.848868 0.0628888 -0.0227312
-0.0223476 0.906883 -0.079749
0.000268979 0.0213251 0.734412
Offset = [-0.000700382, 1.39764, 17.1263]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.848512 0.0687641 -0.0207919
-0.0297134 0.910544 -0.0876276
-0.00367369 0.022368 0.74178
Offset = [-0.0750295, 1.4207, 16.9347]
Guessed background level: 0
[AtlasCreator 18:33:31] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (97.4492%)
second place: 0 (0.0286768%)
Guessed background level: 0
[AtlasCreator 18:33:33] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:33:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG9.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG9.mat --outputVolume /var/tmp/haehn/Slicer3haehn/HNr_YqAtlasCreator/caseG9.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
305 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 198
LowHigh Thresholds: [0,70.8906,198]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
184 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,66.0962,176]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x10fda50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-1.6428, -3.95042, 13.6015]
Center: [-1.61675, 7.30756, 17.8001]
Translation: [-1.0728, -0.339516, 11.6932]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996557 0.0196824 -0.0805407
-0.0124154 0.995887 0.0897542
0.081976 -0.0884453 0.992702
Offset = [0.33878, -2.08596, 13.5729]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.895199 0.0114239 -0.0538334
-0.00459519 0.86868 0.125304
0.05484 -0.124866 0.776548
Offset = [-0.784679, -1.10087, 17.8171]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898459 0.00908197 -0.0640395
0.0385854 0.866259 0.0760804
0.0431014 -0.152374 0.762267
Offset = [-0.433564, -0.0668182, 17.8262]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.894175 0.0094918 -0.0632568
0.03911 0.866227 0.061309
0.0421803 -0.14467 0.763527
Offset = [-0.445556, 0.0865455, 17.7525]
[AtlasCreator 18:37:28] Waiting for Registration to complete..
[AtlasCreator 18:37:33] DEBUG: All outputs exist!
[AtlasCreator 18:37:33] Starting iteration 3...
Warning: In /var/tmp/haehn/SLICER/TRUNK/Slicer3/Libs/MRML/vtkMRMLVolumeArchetypeStorageNode.cxx, line 478
vtkMRMLVolumeArchetypeStorageNode (0x7ff944f025b0): WriteData: removing old version of file /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Background level guess :
first place: 0 (99.6492%)
second place: 68 (0.00519283%)
Guessed background level: 0
[AtlasCreator 18:38:38] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 18:38:40] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:38:40] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
218 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 127
LowHigh Thresholds: [0,44.0234,127]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1743a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [-1.13425, 0.408296, -2.02254]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-0.849886, -1.37964, -1.35971]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997895 0.0647795 -0.00306169
-0.0648289 0.995174 -0.0736583
-0.00172463 0.0737017 0.997279
Offset = [-1.73522, -0.13636, -0.805505]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.959881 0.0425705 -0.0171902
-0.0433112 0.977908 -0.045303
0.0152279 0.0459997 0.784201
Offset = [-1.43045, -0.15497, 2.82478]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.957352 0.047039 -0.0283392
-0.0316169 0.970845 -0.0731508
0.0149218 0.0330301 0.78279
Offset = [-1.01648, 0.138953, 2.91894]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.958794 0.0503403 -0.0182942
-0.0470496 0.969221 -0.0724084
0.00611244 0.0370724 0.782949
Offset = [-1.3277, 0.0204032, 2.98206]
Background level guess :
first place: 0 (99.8355%)
second place: 156 (0.00356523%)
Guessed background level: 0
[AtlasCreator 18:42:43] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 18:42:45] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:42:45] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
269 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,64.1875,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2513a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
0.99863 0.0522642 0.00273905
-0.052336 0.997261 0.0522642
4.33681e-19 -0.052336 0.99863
Offset: [-1.1101, 0.153434, -0.934127]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-0.681013, 1.12689, -1.33772]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0522642 0.997261 -0.052336
0.00273905 0.0522642 0.99863
Singular: 0
Versor: [ -0.026168, 0.000685233, -0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 44 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998814 0.0340702 0.0347853
-0.0345151 0.999329 0.0122696
-0.0343439 -0.0134556 0.999319
Offset = [-1.79084, 0.81021, 0.0798642]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.909002 0.0240284 0.0243245
-0.0246131 0.968558 0.0240296
-0.0237327 -0.0246143 0.793127
Offset = [-1.89559, 1.0356, 3.63294]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.909652 0.0152073 0.0178213
-0.0299547 0.967809 -0.0147367
-0.0226217 -0.0496091 0.785168
Offset = [-1.61504, 1.56781, 3.7888]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.913318 0.0153235 0.0150882
-0.0286787 0.960263 -0.0205517
-0.0234968 -0.0458203 0.786355
Offset = [-1.42093, 1.43073, 3.74934]
Background level guess :
first place: 0 (99.1645%)
second place: 142 (0.0144934%)
Guessed background level: 0
[AtlasCreator 18:46:45] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 18:46:47] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:46:47] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
261 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 167
LowHigh Thresholds: [0,59.6953,167]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2946a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.994522 -0.103956 0.0109262
0.104528 0.989074 -0.103956
1.73472e-18 0.104528 0.994522
Offset: [-1.96109, 1.21563, 1.39928]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-2.51618, -0.840091, 2.06211]
Inverse:
0.994522 0.104528 1.73472e-18
-0.103956 0.989074 0.104528
0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, 0.00273905, 0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.989849 -0.0994339 0.101548
0.102496 0.99441 -0.0253818
-0.0984563 0.0355324 0.994507
Offset = [-3.47108, 0.272813, 1.65008]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.91242 -0.0759588 0.100477
0.0795575 0.968481 -0.032302
-0.0976524 0.0400384 0.777095
Offset = [-4.10696, 0.579842, 6.30319]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.906181 -0.0755284 0.0971108
0.107131 0.971528 -0.0465114
-0.121094 0.0236063 0.772505
Offset = [-3.9739, 0.7677, 6.23526]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907205 -0.076636 0.0925873
0.104352 0.975523 -0.0452793
-0.115539 0.0313174 0.774039
Offset = [-3.92195, 0.591529, 6.21996]
Background level guess :
first place: 0 (99.9963%)
second place: 141 (0.00031002%)
Guessed background level: 0
[AtlasCreator 18:50:50] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 18:50:52] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:50:52] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
377 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.8906,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xe4aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.994522 0.102244 -0.0217327
-0.104528 0.972789 -0.206773
-1.73472e-18 0.207912 0.978148
Offset: [-1.6122, 4.12968, 4.30212]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.24082, 0.490257, 5.42946]
Inverse:
0.994522 -0.104528 -1.73472e-18
0.102244 0.972789 0.207912
-0.0217327 -0.206773 0.978148
Singular: 0
Versor: [ 0.104385, -0.0054706, -0.0520493, 0.993159 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 105 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997287 0.0552187 -0.0486857
-0.0618161 0.987278 -0.146494
0.0399772 0.149106 0.988013
Offset = [-1.47685, 2.51266, 5.45181]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905665 0.0536137 -0.0367243
-0.0560223 0.910703 -0.0680405
0.0329334 0.0699541 0.739718
Offset = [-1.51774, 2.21368, 10.0399]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.906445 0.0558077 -0.0447689
-0.0532916 0.908343 -0.0832087
0.0328604 0.0583796 0.735895
Offset = [-1.33659, 2.25092, 10.1849]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907369 0.0526522 -0.0398423
-0.0520534 0.907168 -0.0886034
0.031598 0.0664601 0.737338
Offset = [-1.46257, 2.22781, 9.8921]
Guessed background level: 0
[AtlasCreator 18:54:57] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 18:54:59] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:54:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case19.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case19.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case19.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
331 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 220
LowHigh Thresholds: [0,81.1562,220]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xd2ca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 0.0522642 -0.00273905
-0.052336 0.997261 -0.0522642
-6.50521e-19 0.052336 0.99863
Offset: [5.41696, 4.3558, 0.825401]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [5.75052, 3.5065, 1.1812]
Inverse:
0.99863 -0.052336 -6.50521e-19
0.0522642 0.997261 0.052336
-0.00273905 -0.0522642 0.99863
Singular: 0
Versor: [ 0.026168, -0.000685233, -0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998119 0.0611862 0.00371099
-0.0611336 0.998046 -0.0129463
-0.00449587 0.012695 0.999909
Offset = [5.19282, 3.857, 1.96471]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.894612 0.0568169 0.00131579
-0.0568138 0.889756 -0.00228888
-0.00144371 0.00221042 0.76607
Offset = [4.98411, 4.38113, 6.00385]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.894674 0.0479135 -0.000268393
-0.0478927 0.885634 -0.0255003
-0.00805209 -0.0132069 0.758314
Offset = [4.98307, 4.55242, 5.99292]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.894337 0.0528517 -0.000749027
-0.0485353 0.883771 -0.0233932
-0.0050667 -0.0106024 0.768834
Offset = [4.91717, 4.67459, 5.73914]
Background level guess :
first place: 0 (99.9893%)
second place: 41 (0.00031002%)
Guessed background level: 0
[AtlasCreator 18:58:53] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 18:58:55] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 18:58:55] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
245 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 157
LowHigh Thresholds: [0,57.2812,157]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x28fba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
0.987688 0.156434 -2.17096e-18
-0.156434 0.987688 -1.37069e-17
-1.92593e-34 1.38778e-17 1
Offset: [-1.06844, -5.69965, -8.15357]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [0.0857696, -5.54402, -8.15357]
Inverse:
0.987688 -0.156434 -1.92593e-34
0.156434 0.987688 1.38778e-17
-2.17096e-18 -1.37069e-17 1
Singular: 0
Versor: [ 6.9175e-18, -5.44419e-19, -0.0784591, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99236 0.123366 0.00177
-0.123367 0.992361 0.000528385
-0.00169129 -0.000742707 0.999998
Offset = [-0.950985, -5.54735, -8.23867]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.926031 0.0386504 -0.0617827
-0.036533 0.892913 0.0350413
0.0630579 -0.032691 0.75719
Offset = [0.184392, -5.09861, -2.42173]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921576 0.0495057 -0.0728629
-0.0718844 0.884991 -0.0245468
0.0489518 -0.0580822 0.745578
Offset = [0.341635, -4.48384, -2.33599]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920241 0.0433395 -0.0732152
-0.0708775 0.884405 -0.0376991
0.0452147 -0.0479239 0.746828
Offset = [0.396329, -4.32055, -2.20931]
Background level guess :
first place: 0 (99.9754%)
second place: 87 (0.000697545%)
Guessed background level: 0
[AtlasCreator 19:02:45] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:02:46] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:02:46] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case20.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case20.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case20.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
274 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,64.5469,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2470a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 -1.45062e-18
1.38778e-17 0.994522 0.104528
0 -0.104528 0.994522
Offset: [-1.22698, -0.969527, 9.03859]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.22698, 0.813487, 8.18471]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 -0.104528
-1.45062e-18 0.104528 0.994522
Singular: 0
Versor: [ -0.052336, -3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999745 -0.00136799 -0.0225371
0.00363762 0.994882 0.100976
0.0222836 -0.101033 0.994634
Offset = [-0.996931, -1.1179, 9.15891]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.965713 0.00899637 -0.0203168
-0.00709282 0.92495 0.091895
0.021057 -0.0917282 0.766482
Offset = [-1.18349, -0.256948, 13.6644]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.973596 0.0102959 -0.0249926
0.0299081 0.92078 0.0591327
0.0123261 -0.0976851 0.758164
Offset = [-1.02009, 0.295597, 13.7458]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.974107 0.0100719 -0.027711
0.0323107 0.916891 0.0628989
0.0156297 -0.095427 0.756294
Offset = [-1.07709, 0.386061, 13.8068]
Guessed background level: 0
[AtlasCreator 19:06:54] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:06:56] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:06:56] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case23.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case23.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case23.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 181
LowHigh Thresholds: [0,64.5703,181]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x125ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.2267, -0.509419, -4.21584]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [1.2267, 2.95759, -6.1053]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 108 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999376 0.000638718 -0.0353152
0.00715446 0.97545 0.220104
0.0345888 -0.22022 0.974837
Offset = [1.62696, -1.32311, -3.55849]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.955854 0.00997315 -0.0250858
-0.00559111 0.886683 0.169036
0.0264102 -0.168834 0.716308
Offset = [1.27845, 1.01781, 0.947067]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.948363 0.0105038 -0.027421
-0.00657427 0.885948 0.108482
0.0282564 -0.184992 0.716855
Offset = [1.23437, 1.70298, 0.852447]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.94609 0.0114339 -0.0254959
-0.00291696 0.88473 0.109989
0.030752 -0.182054 0.714662
Offset = [1.24482, 1.6818, 0.979581]
Background level guess :
first place: 0 (99.606%)
second place: 143 (0.00759549%)
Guessed background level: 0
[AtlasCreator 19:11:03] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:11:05] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:11:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case26.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case26.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case26.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
259 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 171
LowHigh Thresholds: [0,61.1719,171]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x192ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104528 1.45062e-18
0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [-5.47496, -2.08283, -6.85336]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-6.22474, -2.28625, -6.85336]
Inverse:
0.994522 0.104528 0
-0.104528 0.994522 1.38778e-17
1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, 3.63154e-19, 0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996735 -0.0770906 0.0240267
0.076903 0.997001 0.00863603
-0.0246204 -0.0067601 0.999674
Offset = [-6.69618, -1.90363, -5.90217]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.973404 -0.0867048 0.0179996
0.0862927 0.972621 0.0225345
-0.0198818 -0.0208928 0.80967
Offset = [-6.7058, -1.51838, -2.56532]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.972964 -0.0831372 0.004636
0.0884974 0.966866 -0.0116776
-0.0393829 -0.0431536 0.793725
Offset = [-6.22762, -0.690266, -2.26216]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.97883 -0.0849881 0.00168336
0.0948293 0.972136 -0.016724
-0.0366066 -0.0374313 0.799656
Offset = [-6.20498, -0.867375, -2.49793]
Background level guess :
first place: 0 (99.9778%)
second place: 228 (0.00093006%)
Guessed background level: 0
[AtlasCreator 19:14:58] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:15:00] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:15:00] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
340 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 240
LowHigh Thresholds: [0,89.9062,240]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x23e6a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4093
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104385 -0.0054706
0.104528 0.993159 0.0520493
4.33681e-19 -0.052336 0.99863
Offset: [-0.97847, 2.28229, -10.8221]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.8226, 2.97661, -11.2257]
Inverse:
0.994522 0.104528 4.33681e-19
-0.104385 0.993159 -0.052336
-0.0054706 0.0520493 0.99863
Singular: 0
Versor: [ -0.0261411, -0.00137, 0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.994526 -0.103516 -0.0142215
0.103815 0.994349 0.0221717
0.011846 -0.0235267 0.999653
Offset = [-1.25658, 2.68736, -10.7334]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.8788 -0.0667525 0.00425472
0.0665409 0.901343 0.0383918
-0.00680489 -0.0380227 0.727569
Offset = [-2.13295, 3.14417, -6.30479]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.879925 -0.0706864 -0.00175565
0.0518475 0.903489 0.0264472
-0.0172921 -0.0413575 0.726991
Offset = [-2.00145, 3.3859, -6.20864]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.875663 -0.0642831 -0.00354771
0.0530393 0.901096 0.0279031
-0.0195086 -0.044191 0.717326
Offset = [-1.88826, 3.3939, -5.95422]
Guessed background level: 0
[AtlasCreator 19:18:44] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:18:46] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:18:46] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case29.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case29.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case29.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
228 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 172
LowHigh Thresholds: [0,62.9062,172]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x12bba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-7.01625, 0.846444, -6.42471]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-6.45296, 4.38071, -8.31417]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998793 0.0470717 -0.0140522
-0.0429019 0.975172 0.217253
0.0239297 -0.216388 0.976014
Offset = [-6.41165, 0.570367, -5.96966]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 93 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.893045 0.0216217 -0.0269285
-0.0173837 0.878453 0.148711
0.0298404 -0.148154 0.768257
Offset = [-6.69674, 3.20432, -2.60253]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.892315 0.0194461 -0.0245001
-0.0756702 0.880389 0.0735383
0.0375132 -0.186637 0.771659
Offset = [-6.54118, 3.89075, -2.5848]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.896461 0.0192871 -0.0322546
-0.0722367 0.887637 0.0697295
0.0544833 -0.184798 0.772498
Offset = [-6.72404, 3.93598, -2.68807]
Background level guess :
first place: 0 (99.6932%)
second place: 135 (0.00364273%)
Guessed background level: 0
[AtlasCreator 19:22:57] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:22:59] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:22:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
324 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,69.3359,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1167a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 1.45062e-18
1.38778e-17 0.994522 -0.104528
0 0.104528 0.994522
Offset: [-5.88355, 2.95814, -1.83918]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-5.88355, 1.09563, -1.17635]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 0.104528
1.45062e-18 -0.104528 0.994522
Singular: 0
Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 89 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999655 -0.00859681 -0.0248264
0.0066097 0.996849 -0.079041
0.0254277 0.0788496 0.996562
Offset = [-5.53157, 1.46672, -1.17256]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.900966 -0.0193091 -0.0352058
0.0179997 0.968928 -0.037139
0.0358929 0.0364754 0.754312
Offset = [-5.49878, 1.15152, 3.87898]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.901588 -0.0181069 -0.0470023
0.0122458 0.954224 -0.0501819
0.0287757 0.0237479 0.750444
Offset = [-5.31515, 1.6355, 4.1078]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902743 -0.0193586 -0.0421844
0.0163809 0.960839 -0.0599051
0.0224985 0.0269292 0.746923
Offset = [-5.30861, 1.56857, 4.02919]
Background level guess :
first place: 0 (99.9661%)
second place: 125 (0.00100756%)
Guessed background level: 0
[AtlasCreator 19:27:01] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:27:03] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:27:03] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case32.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case32.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case32.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
253 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 162
LowHigh Thresholds: [0,58.4531,162]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xbc0a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [-2.2028, -2.49593, -9.45199]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-2.2028, 0.971078, -11.3414]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999299 -0.0292069 -0.0234287
0.0335883 0.975769 0.216209
0.0165462 -0.216845 0.976066
Offset = [-1.31413, -2.5569, -8.76353]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902219 -0.0308452 -0.0506977
0.03968 0.936185 0.183729
0.0441268 -0.185417 0.83997
Offset = [-1.21626, -1.7767, -6.42671]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.890252 -0.0383551 -0.0758946
0.0527371 0.927183 0.114064
0.0491578 -0.210901 0.742423
Offset = [-1.11551, -0.378719, -4.76695]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.892823 -0.0397092 -0.0755667
0.0483517 0.924576 0.115461
0.0545274 -0.210326 0.736759
Offset = [-1.16803, -0.49163, -4.69433]
Guessed background level: 0
[AtlasCreator 19:30:58] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:31:00] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:31:00] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
224 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 144
LowHigh Thresholds: [0,52.8125,144]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x20a4a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [4.73006, -4.2781, -13.2599]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [5.24999, -1.57114, -14.6095]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 70 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997154 0.0697591 -0.028602
-0.0648115 0.986929 0.14755
0.038521 -0.145276 0.988641
Offset = [5.28258, -3.77565, -11.9285]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920921 0.0455877 -0.0425766
-0.0396508 0.885651 0.131155
0.0481541 -0.129212 0.771175
Offset = [5.30538, -2.20137, -8.77903]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.923244 0.0533642 -0.0448176
-0.0623643 0.888649 0.0547284
0.0348102 -0.16419 0.773714
Offset = [5.35898, -1.75657, -8.83431]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921536 0.0523386 -0.041092
-0.0606016 0.890649 0.057899
0.032338 -0.170766 0.76648
Offset = [5.38677, -1.79232, -8.73706]
Background level guess :
first place: 0 (99.8568%)
second place: 144 (0.00224764%)
Guessed background level: 0
[AtlasCreator 19:35:05] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:35:07] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:35:07] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case36.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case36.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case36.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
273 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,63,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e8da50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4090
Debug: Off
Observers:
none
Matrix:
0.978148 -0.207627 -0.0108813
0.207912 0.976807 0.0511923
8.67362e-19 -0.052336 0.99863
Offset: [-4.28474, -0.0550943, -10.7359]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-5.9466, 0.343766, -11.1395]
Inverse:
0.978148 0.207912 8.67362e-19
-0.207627 0.976807 -0.052336
-0.0108813 0.0511923 0.99863
Singular: 0
Versor: [ -0.0260335, -0.00273624, 0.104493, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.987251 -0.151819 0.0478156
0.146279 0.983816 0.103485
-0.0627527 -0.0951711 0.993481
Offset = [-5.87109, -0.904189, -9.26909]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891986 -0.155604 0.0493123
0.150169 0.955266 0.09946
-0.0639822 -0.0907208 0.76617
Offset = [-6.16483, -0.67235, -5.3634]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.899064 -0.156927 0.0455417
0.121503 0.95065 0.0671057
-0.0879134 -0.112738 0.753199
Offset = [-6.12195, -0.599446, -5.31974]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.888755 -0.15501 0.048259
0.125208 0.947913 0.0647802
-0.0812079 -0.110257 0.752091
Offset = [-6.19142, -0.568959, -5.14796]
Background level guess :
first place: 0 (99.9645%)
second place: 127 (0.000697545%)
Guessed background level: 0
[AtlasCreator 19:38:58] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:39:01] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:39:01] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case40.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case40.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case40.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 204
LowHigh Thresholds: [0,73.7344,204]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1b4ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 0.0054706
-0.052336 0.993159 0.104385
-8.67362e-19 -0.104528 0.994522
Offset: [2.38434, -2.58934, -13.5911]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [2.8595, -0.736762, -14.4449]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0520493 0.993159 -0.104528
0.0054706 0.104385 0.994522
Singular: 0
Versor: [ -0.052318, 0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99926 0.03814 0.00492895
-0.0384572 0.990999 0.128229
6.07293e-06 -0.128324 0.991732
Offset = [2.1582, -2.75965, -13.3498]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.897393 0.0141755 -0.0418842
-0.0106006 0.908074 0.0843733
0.0429286 -0.0838468 0.763177
Offset = [2.7407, -1.06292, -8.29632]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.897825 0.012675 -0.0537116
0.0126189 0.901164 0.0272641
0.0374057 -0.108527 0.75355
Offset = [3.15034, -0.26809, -8.12012]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898209 0.0168636 -0.050145
0.00178101 0.904994 0.0278812
0.0399262 -0.10743 0.755145
Offset = [3.06641, -0.461299, -8.2156]
Background level guess :
first place: 0 (99.8872%)
second place: 69 (0.00271267%)
Guessed background level: 0
[AtlasCreator 19:42:49] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:42:51] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:42:51] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case41.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case41.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case41.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 139
LowHigh Thresholds: [0,50.0625,139]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x14eba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 -1.45062e-18
1.38778e-17 0.994522 0.104528
0 -0.104528 0.994522
Offset: [-3.2165, -0.71895, -10.7036]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-3.2165, 1.06406, -11.5575]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 -0.104528
-1.45062e-18 0.104528 0.994522
Singular: 0
Versor: [ -0.052336, -3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 110 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999755 -0.00266502 0.0219584
0.00110227 0.997485 0.070876
-0.022092 -0.0708344 0.997243
Offset = [-4.07219, -0.140291, -10.8597]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905246 -0.000447895 0.034972
-0.00255312 0.934171 0.08572
-0.0348816 -0.0857568 0.767306
Offset = [-4.29949, 0.260145, -6.0425]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908096 -0.000445246 0.0252405
-0.0125835 0.93281 0.037212
-0.0598173 -0.101778 0.756492
Offset = [-4.03151, 0.532107, -6.05819]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904404 0.00213699 0.0130159
-0.0170701 0.937743 0.0334424
-0.0564595 -0.102478 0.754012
Offset = [-3.816, 0.598198, -6.11241]
Guessed background level: 0
[AtlasCreator 19:47:11] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:47:13] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:47:13] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case42.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case42.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case42.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,70.1172,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xd2aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [-0.495337, -1.74801, -18.4511]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [0.0245977, 0.958952, -19.8007]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999124 0.000564281 -0.0418449
0.00616772 0.987004 0.160575
0.0413918 -0.160693 0.986136
Offset = [0.487767, -1.51904, -17.4603]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902295 0.000900841 -0.014562
0.00145345 0.92438 0.160857
0.0145173 -0.160861 0.754149
Offset = [-0.23392, -0.709578, -14.0475]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.900728 -0.000732719 -0.0334997
-0.0156629 0.913873 0.0940614
0.0107138 -0.184153 0.73915
Offset = [0.0150069, 0.240275, -13.8475]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.895844 0.000897447 -0.0252364
-0.0221116 0.91876 0.104948
0.00420527 -0.1844 0.738978
Offset = [0.0963616, -0.0551909, -13.9046]
Background level guess :
first place: 0 (99.7911%)
second place: 120 (0.00356523%)
Guessed background level: 0
[AtlasCreator 19:51:10] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:51:12] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:51:12] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case46.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case46.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case46.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
226 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,54.4219,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x26c2a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [4.80114, 3.45362, -1.75234]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [4.62163, -0.417173, -0.625005]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999355 -0.013047 0.0334476
0.0184365 0.985908 -0.166272
-0.0308069 0.166781 0.985513
Offset = [3.95605, 2.2374, -0.633253]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.918969 -0.0160587 0.0192944
0.0187669 0.934505 -0.149568
-0.016672 0.149883 0.783703
Offset = [3.84875, 2.96144, 1.99073]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.914469 -0.0171572 0.00899395
-0.0121881 0.928823 -0.157079
-0.0495049 0.148825 0.783891
Offset = [4.25322, 3.05637, 1.90802]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.914085 -0.0145459 0.00680027
-0.0109361 0.932912 -0.154218
-0.0502678 0.145898 0.786019
Offset = [4.42116, 2.99449, 1.95616]
Guessed background level: 0
[AtlasCreator 19:55:14] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:55:16] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:55:16] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case47.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case47.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case47.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
287 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,63.25,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1ec3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [-5.77275, -0.841427, 0.0871397]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-6.00286, -3.74667, 1.00738]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999836 -0.0167231 0.00697212
0.0174508 0.992335 -0.12234
-0.00487277 0.122442 0.992464
Offset = [-6.35181, -2.25076, -0.186674]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.916794 -0.00786247 0.00923237
0.00834452 0.866 -0.0533909
-0.00879909 0.053464 0.768875
Offset = [-6.69931, -1.72775, 5.31787]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.917881 -0.00266276 0.00634831
0.0337754 0.869759 -0.06859
-0.0222916 0.0580452 0.76658
Offset = [-6.53569, -1.52088, 5.40914]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.919622 -0.00742777 -0.00362854
0.0294651 0.868809 -0.0602697
-0.0174125 0.0544279 0.766409
Offset = [-6.43998, -1.64008, 5.27403]
Guessed background level: 0
[AtlasCreator 19:59:17] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 19:59:19] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 19:59:19] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case48.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case48.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case48.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
205 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 133
LowHigh Thresholds: [0,47.8047,133]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2132a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.994522 0.103956 -0.0109262
-0.104528 0.989074 -0.103956
-8.67362e-19 0.104528 0.994522
Offset: [0.508052, 1.10798, -11.41]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [1.0803, -0.62038, -10.7471]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.103956 0.989074 0.104528
-0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, -0.00273905, -0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 70 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995252 0.0843309 -0.0486048
-0.0870554 0.994573 -0.0569657
0.0435371 0.0609265 0.997192
Offset = [0.939644, -1.49394, -10.6245]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 83 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.937674 0.0810734 -0.0425737
-0.0818548 0.894282 -0.0169401
0.0410513 0.0203538 0.760098
Offset = [0.816268, -0.0696011, -4.87338]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93907 0.0691081 -0.0483805
-0.0383096 0.893575 -0.0790235
0.0376585 -0.0123856 0.749822
Offset = [0.961388, 0.964165, -4.94061]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.938945 0.0762627 -0.0492203
-0.0339892 0.89873 -0.0824142
0.03671 -0.00510892 0.753827
Offset = [0.99665, 1.03533, -5.16012]
Background level guess :
first place: 0 (99.7032%)
second place: 148 (0.00596788%)
Guessed background level: 0
[AtlasCreator 20:03:32] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:03:34] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:03:34] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,63.2109,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1778a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [1.23096, 2.08702, -17.0622]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [1.75089, 4.79398, -18.4118]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998008 0.0513259 0.0366838
-0.0555575 0.990525 0.125594
-0.02989 -0.127382 0.991403
Offset = [0.724084, 2.37828, -17.0673]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.946512 0.0367491 0.0352743
-0.0411868 0.966418 0.134673
-0.0299737 -0.135951 0.83119
Offset = [0.443782, 2.7689, -13.4909]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.951672 0.0324864 0.0222074
-0.0628039 0.957361 0.0900264
-0.0483289 -0.15576 0.808138
Offset = [0.816053, 3.44772, -13.3881]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.943618 0.0326825 0.0226919
-0.0568529 0.951178 0.0923434
-0.0405716 -0.159963 0.806714
Offset = [0.689334, 3.44315, -13.1778]
Background level guess :
first place: 0 (99.5194%)
second place: 159 (0.00658792%)
Guessed background level: 0
[AtlasCreator 20:07:28] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:07:31] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:07:31] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case51.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case51.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case51.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
265 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 174
LowHigh Thresholds: [0,63.7031,174]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x284ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 -0.0108813
-0.052336 0.976807 -0.207627
8.67362e-19 0.207912 0.978148
Offset: [1.76174, 0.634324, 6.94009]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [1.94554, -3.07257, 8.06743]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0511923 0.976807 0.207912
-0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99882 0.039372 0.0284352
-0.0338786 0.984352 -0.172927
-0.0347988 0.17176 0.984524
Offset = [1.40507, -0.103885, 7.54457]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 59 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891486 0.025823 0.0235855
-0.0223537 0.95161 -0.137063
-0.0268963 0.136452 0.783001
Offset = [0.911896, -0.526059, 11.6588]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.899504 0.0280504 0.0285063
-0.0399307 0.957443 -0.151265
-0.045079 0.133108 0.784765
Offset = [0.762653, -0.416379, 11.6645]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.892369 0.0296971 0.0227833
-0.0353003 0.956501 -0.151979
-0.0346074 0.136653 0.779135
Offset = [0.970715, -0.478783, 11.8402]
Background level guess :
first place: 0 (99.921%)
second place: 111 (0.00124008%)
Guessed background level: 0
[AtlasCreator 20:11:31] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:11:33] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:11:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case53.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case53.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case53.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 195
LowHigh Thresholds: [0,72.1875,195]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x19aca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [1.47188, 2.21278, -7.24042]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [1.75625, 0.424838, -6.5776]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999265 0.034339 0.0170431
-0.0335619 0.998469 -0.0439618
-0.0185266 0.0433575 0.998888
Offset = [0.948577, 1.03659, -6.55331]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.934688 0.0290617 -0.0038067
-0.0291665 0.945944 -0.0311985
0.00289655 0.0312961 0.793014
Offset = [1.18852, 2.03519, -2.21346]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.936925 0.027983 -0.00370624
-0.0230425 0.938564 -0.0561048
-0.0211507 0.00986395 0.782419
Offset = [1.18719, 2.41396, -2.11968]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 59 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.939361 0.0398245 -0.00884343
-0.0383041 0.932548 -0.0612663
-0.0145883 0.012938 0.78645
Offset = [1.17688, 2.47766, -2.19067]
Guessed background level: 0
[AtlasCreator 20:15:32] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:15:34] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:15:34] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case54.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case54.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case54.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
295 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 196
LowHigh Thresholds: [0,73.4062,196]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1502a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-3.47981, 1.37458, -2.48147]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-2.91652, 4.90885, -4.37093]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997715 0.0413008 0.0534785
-0.0498964 0.984017 0.170941
-0.0455638 -0.173219 0.983829
Offset = [-4.09139, 2.08912, -2.60722]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.889892 0.0111967 0.00981582
-0.0122305 0.850183 0.112508
-0.00849304 -0.112616 0.731948
Offset = [-3.71476, 4.56283, 1.43931]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.88526 0.0179465 0.00578781
-0.0342669 0.845219 0.0479102
-0.0179701 -0.131269 0.719081
Offset = [-3.60061, 5.5541, 1.81754]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.886225 0.0110807 -0.00178951
-0.0302167 0.844702 0.0390413
-0.0142697 -0.13153 0.716763
Offset = [-3.54012, 5.69182, 1.96817]
Background level guess :
first place: 0 (99.8487%)
second place: 86 (0.00263517%)
Guessed background level: 0
[AtlasCreator 20:19:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:19:31] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:19:31] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case57.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case57.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case57.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
264 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 169
LowHigh Thresholds: [0,60.8125,169]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1aa8a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [-1.61016, 1.97337, -0.302534]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.84027, -0.931869, 0.617707]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999419 -0.002384 0.0339908
0.00603126 0.994175 -0.107607
-0.0335363 0.107749 0.993612
Offset = [-2.43683, 0.730748, 0.384943]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 128 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.926549 -0.0140667 0.0173
0.0151899 0.928749 -0.0666005
-0.0163228 0.0668467 0.758509
Offset = [-2.54677, 1.19914, 4.47243]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924189 -0.0113522 0.0108177
0.0162088 0.925462 -0.0904003
-0.0221716 0.0543928 0.75613
Offset = [-2.17852, 1.48804, 4.21339]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.925458 -0.00819648 0.018403
0.0159177 0.919708 -0.0982265
-0.0254201 0.0605668 0.7511
Offset = [-2.33926, 1.27721, 4.58764]
Guessed background level: 0
[AtlasCreator 20:23:52] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:23:55] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:23:55] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case59.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case59.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case59.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,70.0312,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1683a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [1.78539, 0.910541, -4.16437]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [2.06976, -0.877399, -3.50154]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997688 0.0627011 0.0262121
-0.0594018 0.991948 -0.111849
-0.0330141 0.110033 0.993379
Offset = [1.16247, 0.7372, -4.30375]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911869 0.0583725 0.0135033
-0.0578567 0.888426 -0.0358689
-0.0155657 0.0350232 0.765462
Offset = [0.983816, -0.0214214, 1.65309]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.91475 0.0585579 0.00405409
-0.0463348 0.893825 -0.0608071
-0.0341229 0.0226893 0.763602
Offset = [1.29707, 0.489803, 1.39779]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915769 0.0614816 -0.00423523
-0.0479822 0.897111 -0.0560698
-0.0297303 0.0282656 0.764008
Offset = [1.363, 0.532598, 1.39955]
Guessed background level: 0
[AtlasCreator 20:27:53] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:27:55] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:27:55] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case60.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case60.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case60.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
338 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 239
LowHigh Thresholds: [0,90.25,239]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xa88a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.978148 0.207912 -2.88535e-18
-0.207912 0.978148 -1.35745e-17
-1.92593e-34 1.38778e-17 1
Offset: [-3.21887, 0.756172, -1.50105]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.67625, 0.923195, -1.50105]
Inverse:
0.978148 -0.207912 -1.92593e-34
0.207912 0.978148 1.38778e-17
-2.88535e-18 -1.35745e-17 1
Singular: 0
Versor: [ 6.90088e-18, -7.25312e-19, -0.104528, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.987761 0.152889 0.0308638
-0.15437 0.986576 0.0532653
-0.0223058 -0.0573779 0.998103
Offset = [-2.59903, -0.141131, -0.622398]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 92 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.883419 0.0329118 -0.058626
-0.0297914 0.89905 0.0533275
0.0602716 -0.0514603 0.717936
Offset = [-1.70034, 0.871447, 4.66707]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.885573 0.0306902 -0.0536559
-0.0245407 0.892686 0.00904942
0.0456924 -0.0791844 0.711089
Offset = [-1.60962, 1.62996, 4.70521]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.883709 0.0307561 -0.0649607
-0.0311071 0.891735 0.00840702
0.0531923 -0.0779017 0.711231
Offset = [-1.37256, 1.64941, 4.52317]
Background level guess :
first place: 0 (99.929%)
second place: 112 (0.00186012%)
Guessed background level: 0
[AtlasCreator 20:32:07] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:32:09] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:32:09] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case61.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case61.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case61.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,53.9062,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x154ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-1.3007, -0.681231, 4.22384]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.4802, -4.55202, 5.35118]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996992 -0.0183589 0.0753029
0.0380399 0.962387 -0.269008
-0.0675318 0.271063 0.96019
Offset = [-2.65546, -0.195921, 4.73151]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.954406 -0.0168226 0.0635284
0.0308995 0.891896 -0.227613
-0.0580007 0.229084 0.768543
Offset = [-2.71093, -0.287514, 8.24223]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.948019 -0.019923 0.0493937
0.0506984 0.886934 -0.23299
-0.079959 0.218885 0.759173
Offset = [-2.37796, 0.15774, 8.4858]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.946645 -0.0298078 0.0455688
0.0600145 0.888594 -0.24029
-0.0775732 0.221655 0.750674
Offset = [-2.178, 0.346599, 8.4947]
Background level guess :
first place: 0 (99.9685%)
second place: 147 (0.000852555%)
Guessed background level: 0
[AtlasCreator 20:36:10] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:36:13] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:36:13] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case62.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case62.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case62.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
252 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,62.1562,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x28c6a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-3.48841, 7.21722, -1.54295]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-3.48841, 4.40001, -0.622713]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 81 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999649 -0.0246195 -0.00979787
0.0235063 0.994616 -0.100928
0.0122299 0.100662 0.994845
Offset = [-3.298, 5.50542, -1.2258]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924711 -0.028045 0.00293188
0.027971 0.881484 0.0227952
-0.00356926 -0.0227041 0.732516
Offset = [-3.98687, 4.17715, 5.96633]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.91884 -0.0242958 -0.0203774
0.0152993 0.884032 -0.0416806
-0.0167386 -0.0350558 0.740311
Offset = [-3.35983, 5.73252, 5.34325]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.922297 -0.0227075 -0.0143919
0.0149014 0.884649 -0.0348792
-0.0146455 -0.0391737 0.741887
Offset = [-3.3953, 5.42004, 5.21878]
Background level guess :
first place: 0 (99.5161%)
second place: 137 (0.00713046%)
Guessed background level: 0
[AtlasCreator 20:40:17] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:40:19] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:40:19] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/case8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
263 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 160
LowHigh Thresholds: [0,58.2422,160]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x14e4a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [0.494104, -1.06111, 7.11327]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [0.214029, -3.01295, 7.77609]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998927 -0.0462483 0.00236524
0.0462719 0.994791 -0.0908334
0.00184797 0.0908454 0.995863
Offset = [-0.102973, -0.896218, 7.89357]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.840118 -0.0315759 -0.0179574
0.0309235 0.97026 -0.0355148
0.0190589 0.034936 0.748754
Offset = [-0.0654634, -1.36818, 12.156]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.844323 -0.0324782 -0.028731
0.0129536 0.967054 -0.0723958
-0.00046158 0.0397117 0.75754
Offset = [0.361823, -0.629228, 11.9469]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.842651 -0.0292581 -0.0280229
0.0123959 0.972311 -0.0628106
0.00558322 0.0276884 0.751072
Offset = [0.204485, -1.07399, 12.0823]
Background level guess :
first place: 0 (99.7564%)
second place: 38 (0.00302269%)
Guessed background level: 0
[AtlasCreator 20:44:08] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:44:10] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:44:10] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG1.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG1.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG1.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
347 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 234
LowHigh Thresholds: [0,86.4844,234]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xc00a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
0.994522 0.104528 -1.45062e-18
-0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [0.759406, -2.7171, 5.13117]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [1.52634, -2.59317, 5.13117]
Inverse:
0.994522 -0.104528 0
0.104528 0.994522 1.38778e-17
-1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, -3.63154e-19, -0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 67 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.994371 0.0497028 -0.0935735
-0.0498672 0.998756 0.000582436
0.093486 0.00408709 0.995612
Offset = [2.71074, -1.83311, 5.23185]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.901466 0.049626 -0.0744052
-0.0496293 0.950228 0.00180633
0.074403 0.00189358 0.792815
Offset = [1.90298, -1.4331, 9.39737]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.903867 0.0526327 -0.0827876
-0.0304211 0.952946 0.00298245
0.0738949 -0.000160905 0.79689
Offset = [2.24225, -1.49252, 9.31736]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.903102 0.0517586 -0.0764401
-0.023573 0.952788 0.00511973
0.0711197 0.00359445 0.803967
Offset = [2.02909, -1.47825, 9.03316]
Background level guess :
first place: 0 (99.7627%)
second place: 186 (0.00410776%)
Guessed background level: 0
[AtlasCreator 20:48:06] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:48:09] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:48:09] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 215
LowHigh Thresholds: [0,80.8828,215]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1059a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [3.52416, 3.59918, 15.7265]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [3.29405, 0.693933, 16.6467]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997794 -0.0633443 -0.0198584
0.0614768 0.994598 -0.0836372
0.0250491 0.0822319 0.996298
Offset = [3.82436, 2.31931, 16.7824]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.893667 -0.058019 -0.0226496
0.0562566 0.939095 -0.0719325
0.0267284 0.0705187 0.765844
Offset = [3.48402, 2.55052, 21.3967]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.893634 -0.0571086 -0.0218198
0.048101 0.932726 -0.127527
0.000421587 0.0512178 0.752379
Offset = [3.6282, 3.23685, 21.6508]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891916 -0.0575951 -0.0221475
0.04899 0.931204 -0.126073
-0.000826937 0.0502346 0.759376
Offset = [3.65703, 3.31975, 21.5366]
Background level guess :
first place: 0 (99.8225%)
second place: 6 (0.00767299%)
Guessed background level: 0
[AtlasCreator 20:52:04] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:52:06] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:52:06] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG11.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG11.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG11.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.7344,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1f49a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4054
Debug: Off
Observers:
none
Matrix:
1 -1.38018e-17 1.45062e-18
1.38778e-17 0.994522 -0.104528
0 0.104528 0.994522
Offset: [3.46619, -0.583021, 8.95408]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [3.46619, -2.44552, 9.61691]
Inverse:
1 1.38778e-17 0
-1.38018e-17 0.994522 0.104528
1.45062e-18 -0.104528 0.994522
Singular: 0
Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 137 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999708 0.0118689 0.0210268
-0.0105217 0.997954 -0.0630616
-0.0217323 0.0628219 0.997788
Offset = [3.22282, -0.657943, 10.8008]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.884082 0.00938209 0.0220826
-0.00833799 0.917878 -0.0469075
-0.0224976 0.0467099 0.758639
Offset = [2.371, -0.662516, 14.2435]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.884333 0.0160859 0.0166454
-0.0107874 0.921146 -0.0737212
-0.0529325 0.0328187 0.762533
Offset = [2.52053, -0.484009, 13.847]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.886661 0.0135112 0.0146691
-0.0167313 0.923414 -0.0666643
-0.0508752 0.0306537 0.759359
Offset = [2.65609, -0.567605, 13.873]
Guessed background level: 0
[AtlasCreator 20:56:21] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 20:56:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 20:56:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
321 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.5,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x18bfa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-1.37392, 2.3441, 0.263053]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.37392, -0.473109, 1.18329]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999823 -0.0163012 0.00943787
0.017327 0.992453 -0.121396
-0.00738774 0.121538 0.992559
Offset = [-1.18861, 1.40759, 0.273154]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.865843 -0.0099805 0.0199395
0.0102057 0.885389 -0.011222
-0.0198252 0.0114227 0.723979
Offset = [-2.21979, 0.703913, 7.06613]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.868599 -0.00571782 0.0109311
-0.0132435 0.880538 -0.0592953
-0.0520178 -0.00750398 0.724902
Offset = [-1.93297, 1.53937, 6.81415]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.866972 -0.00561014 0.00792464
-0.0143058 0.881601 -0.0575944
-0.0517617 -0.012142 0.719503
Offset = [-1.8911, 1.64599, 6.79735]
Background level guess :
first place: 0 (99.7555%)
second place: 81 (0.00325521%)
Guessed background level: 0
[AtlasCreator 21:00:31] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:00:34] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:00:34] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG13.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG13.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG13.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.0938,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e80a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [-1.01018, 0.924706, 11.4168]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.29025, -1.02714, 12.0796]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 252 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998441 -0.0134743 0.0541747
0.0167092 0.998076 -0.0597098
-0.053266 0.0605219 0.996745
Offset = [-1.2643, -0.637962, 13.3414]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 67 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.930845 -0.0150837 0.0471937
0.0165445 0.942143 -0.0307165
-0.0467016 0.0314596 0.791944
Offset = [-2.08699, -0.252221, 16.2895]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932824 -0.0162629 0.0337195
0.0310465 0.936041 -0.0701765
-0.0621202 0.0285006 0.778748
Offset = [-1.97355, 0.384045, 16.4371]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928731 -0.0202669 0.0363195
0.0267739 0.944784 -0.068059
-0.0634268 0.0245382 0.778834
Offset = [-1.83617, 0.308184, 16.2201]
Background level guess :
first place: 0 (98.828%)
second place: 187 (0.0134859%)
Guessed background level: 0
[AtlasCreator 21:05:23] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:05:26] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:05:26] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
348 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,80.2812,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x213ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.15473, 3.21759, 12.7002]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [3.15473, -0.566491, 13.8276]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999985 0.00179583 0.00523335
-0.000617102 0.976159 -0.217055
-0.00549837 0.217049 0.976145
Offset = [2.64352, 3.03018, 13.7841]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.937401 0.0049582 0.0152196
-0.00195471 0.964062 -0.191341
-0.0158871 0.191286 0.82438
Offset = [2.34625, 2.57075, 17.0393]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.941006 -0.00309161 -0.00327028
0.0122735 0.963703 -0.196127
-0.0421451 0.198073 0.822979
Offset = [2.89026, 2.7878, 17.0839]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.939558 0.000614011 -0.000848138
0.0105436 0.967966 -0.199348
-0.038047 0.201858 0.82297
Offset = [2.55987, 2.72661, 17.1287]
Background level guess :
first place: 0 (99.838%)
second place: 81 (0.00387525%)
Guessed background level: 0
[AtlasCreator 21:09:27] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:09:29] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:09:29] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 186
LowHigh Thresholds: [0,69.8438,186]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xcf6a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 -0.00818715
0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [0.693446, -4.1386, -2.93395]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [0.177804, -1.59554, -4.28357]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 -0.156434
-0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, -0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998099 -0.0539898 -0.0297278
0.0574416 0.989697 0.131153
0.0223405 -0.132612 0.990916
Offset = [1.03248, -3.07857, -2.58682]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.929118 -0.0445667 -0.0283362
0.0475196 0.931626 0.113891
0.0230438 -0.115079 0.795532
Offset = [0.752433, -2.42853, 1.26788]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.926183 -0.0426218 -0.0272428
0.0977134 0.932156 0.0376479
0.00798621 -0.144682 0.803882
Offset = [0.554436, -1.30388, 1.08028]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928792 -0.0390353 -0.0270444
0.102077 0.937039 0.0384808
0.00629971 -0.142417 0.798665
Offset = [0.568418, -1.30875, 1.05241]
Guessed background level: 0
[AtlasCreator 21:13:21] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:13:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:13:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG16.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG16.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG16.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 225
LowHigh Thresholds: [0,84.6094,225]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x267fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-1.76582, 3.30212, -5.23173]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.94533, -0.568675, -4.10439]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998925 -0.0200727 -0.0417735
0.0141628 0.990436 -0.137245
0.0441288 0.136506 0.989656
Offset = [-0.486733, 1.20127, -4.38135]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.870298 -0.024882 -0.0309315
0.0239309 0.867471 -0.0307486
0.0316731 0.0299842 0.719134
Offset = [-1.89717, 0.935176, 1.84675]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878498 -0.0221147 -0.0431856
0.0480037 0.862849 -0.08584
0.0179894 0.0171571 0.712911
Offset = [-1.62747, 1.76838, 1.56824]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.874814 -0.0217152 -0.0387844
0.043147 0.864006 -0.0824168
0.0155653 0.023565 0.714231
Offset = [-1.7117, 1.69605, 1.68171]
Background level guess :
first place: 0 (99.6543%)
second place: 214 (0.00496032%)
Guessed background level: 0
[AtlasCreator 21:17:22] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:17:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:17:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG17.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG17.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG17.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
373 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 246
LowHigh Thresholds: [0,90.8516,246]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x13eba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 -0.0108813
-0.052336 0.976807 -0.207627
8.67362e-19 0.207912 0.978148
Offset: [4.89768, 3.62303, 13.3169]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [5.08147, -0.0838646, 14.4443]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0511923 0.976807 0.207912
-0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998516 0.0491356 0.0234663
-0.0454315 0.989335 -0.13839
-0.030016 0.137119 0.9901
Offset = [4.13637, 2.71914, 14.1003]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915419 0.0493457 0.0117653
-0.0474474 0.940323 -0.12753
-0.0179489 0.126807 0.779501
Offset = [4.08069, 3.31421, 18.2361]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.912739 0.0414603 -0.00802297
-0.0369944 0.937855 -0.161692
-0.0388814 0.111509 0.770172
Offset = [4.29231, 3.64047, 18.1576]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.916624 0.0424713 -0.0074779
-0.0407808 0.939683 -0.166053
-0.0423468 0.111928 0.76952
Offset = [4.28513, 3.76277, 18.1067]
Guessed background level: 0
[AtlasCreator 21:21:21] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:21:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:21:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
280 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 201
LowHigh Thresholds: [0,73.75,201]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1cc3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 0.0163519
-0.104528 0.982278 0.155578
1.73472e-18 -0.156434 0.987688
Offset: [3.81, -2.95219, -2.10303]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [4.85273, -0.20414, -3.45265]
Inverse:
0.994522 -0.104528 1.73472e-18
0.103242 0.982278 -0.156434
0.0163519 0.155578 0.987688
Singular: 0
Versor: [ -0.0783516, 0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.993881 0.0983985 -0.0501903
-0.0908537 0.986642 0.135214
0.0628247 -0.129826 0.989544
Offset = [4.64577, -2.72927, -2.41158]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 64 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.938201 0.0743957 -0.0585701
-0.0670958 0.892092 0.118022
0.0668082 -0.113562 0.786924
Offset = [4.71064, -1.6802, 2.40337]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.945268 0.0835894 -0.0739005
-0.00695162 0.891338 0.0803943
0.0547455 -0.141824 0.786824
Offset = [5.11021, -1.03032, 2.37679]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.943832 0.0832407 -0.076211
-0.0117847 0.890546 0.067476
0.0643343 -0.131759 0.789166
Offset = [5.15401, -0.963034, 2.56866]
Guessed background level: 0
[AtlasCreator 21:25:37] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:25:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:25:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
266 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2812,177]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2931a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.76748, -3.10765, -0.688435]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [1.76748, 0.359355, -2.57789]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999844 0.0105044 -0.0141656
-0.00737064 0.978637 0.205465
0.0160212 -0.205329 0.978562
Offset = [1.94872, -3.08353, -0.959248]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.943013 -0.00152643 -0.00429372
0.00216794 0.90674 0.153622
0.00400825 -0.15363 0.778719
Offset = [1.71326, -1.22932, 3.13666]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.9383 -0.00569792 -0.0130817
-0.000633858 0.908149 0.0818751
-0.00462448 -0.174878 0.761614
Offset = [1.84223, -0.381978, 3.55246]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.941252 -0.00583345 -0.0168186
-0.00346481 0.901023 0.0875384
-0.00422255 -0.180994 0.761161
Offset = [2.08506, -0.496266, 3.42762]
Background level guess :
first place: 0 (99.81%)
second place: 65 (0.00279018%)
Guessed background level: 0
[AtlasCreator 21:29:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:29:32] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:29:32] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
294 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,69.1875,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xc8fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [4.09227, 3.24515, 14.8296]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [3.8122, 1.29331, 15.4925]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99951 -0.0312947 -0.00107524
0.031081 0.995688 -0.0874062
0.00380596 0.0873299 0.996172
Offset = [3.90049, 2.44237, 15.1134]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.901657 -0.0358048 -0.00970364
0.0354562 0.923317 -0.0339836
0.0109087 0.0336162 0.773387
Offset = [4.17033, 2.32526, 19.1127]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89998 -0.0294191 -0.0159578
0.0550854 0.924335 -0.0431202
-0.0149811 0.0264328 0.766076
Offset = [4.11352, 2.46004, 19.3986]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.900478 -0.0278962 -0.0223682
0.0574794 0.924989 -0.0492235
-0.00958036 0.0309569 0.764068
Offset = [4.39549, 2.74226, 19.5837]
Background level guess :
first place: 0 (99.9727%)
second place: 101 (0.0016276%)
Guessed background level: 0
[AtlasCreator 21:33:20] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:33:23] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:33:23] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 227
LowHigh Thresholds: [0,84.7656,227]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x17dfa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.987688 -0.15622 -0.00818715
0.156434 0.986335 0.0516916
8.67362e-19 -0.052336 0.99863
Offset: [-1.47426, 2.0653, 9.07163]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-2.73112, 2.6226, 8.66803]
Inverse:
0.987688 0.156434 8.67362e-19
-0.15622 0.986335 -0.052336
-0.00818715 0.0516916 0.99863
Singular: 0
Versor: [ -0.0260963, -0.00205382, 0.0784322, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.988465 -0.145508 0.0419917
0.143532 0.988539 0.0467876
-0.0483184 -0.0402208 0.998022
Offset = [-2.97784, 2.06642, 8.7702]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.894336 -0.12523 0.0302563
0.124172 0.910027 0.0346368
-0.0343414 -0.0305911 0.812558
Offset = [-3.0386, 3.53354, 13.0298]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.900388 -0.127266 0.0303716
0.0945744 0.904452 -0.0173589
-0.0647497 -0.0685002 0.811677
Offset = [-2.885, 3.83903, 12.878]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.894736 -0.124687 0.0223776
0.102166 0.905165 -0.0195778
-0.0537924 -0.068057 0.805242
Offset = [-2.82842, 3.81955, 13.1249]
Background level guess :
first place: 0 (99.8485%)
second place: 76 (0.00217014%)
Guessed background level: 0
[AtlasCreator 21:37:15] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:37:18] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:37:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG4.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG4.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG4.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 205
LowHigh Thresholds: [0,75.9375,205]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2585a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 -0.00818715
-0.052336 0.986335 -0.15622
8.67362e-19 0.156434 0.987688
Offset: [0.730305, 0.888847, 17.64]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [0.964707, -1.85249, 18.5602]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0516916 0.986335 0.156434
-0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, -0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998453 -0.00138318 -0.055584
-0.00849328 0.984164 -0.177055
0.0549486 0.177253 0.98263
Offset = [1.28979, 1.22174, 18.8245]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.834629 -0.00282671 -0.0325395
-0.00125074 0.938225 -0.12461
0.0326381 0.124584 0.704943
Offset = [0.539723, 0.652697, 23.8573]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.825195 0.00324041 -0.0322598
0.0067986 0.935428 -0.135219
0.0257791 0.108892 0.6976
Offset = [0.685727, 0.916426, 24.1831]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.833411 0.00390605 -0.0360652
0.00146109 0.936591 -0.134317
0.0333304 0.109357 0.702489
Offset = [0.693807, 1.07542, 23.9436]
Background level guess :
first place: 0 (99.959%)
second place: 76 (0.00139509%)
Guessed background level: 0
[AtlasCreator 21:41:17] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:41:20] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:41:20] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,82.5,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x288aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.43444, 6.09452, 4.79824]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [3.43444, 2.31044, 5.92558]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999438 -0.0328515 0.00667305
0.0334882 0.987427 -0.154488
-0.00151397 0.154625 0.987972
Offset = [3.24447, 4.52009, 5.33357]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908555 -0.0183468 0.00060712
0.0183041 0.896408 -0.108634
0.00138966 0.108627 0.735294
Offset = [3.01705, 5.46796, 10.2638]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915685 -0.0229465 -0.00573892
0.024449 0.889371 -0.135614
-0.0113389 0.092502 0.736972
Offset = [3.23645, 5.95093, 10.3154]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915345 -0.0264939 -0.00197292
0.0288933 0.888857 -0.137123
-0.0134004 0.0964409 0.736356
Offset = [3.01217, 5.91342, 10.35]
Background level guess :
first place: 0 (99.998%)
second place: 84 (0.00031002%)
Guessed background level: 0
[AtlasCreator 21:45:15] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:45:17] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:45:17] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG6.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG6.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG6.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
286 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 209
LowHigh Thresholds: [0,77.25,209]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1ea9a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 -0.0108813
0.052336 0.976807 0.207627
8.67362e-19 -0.207912 0.978148
Offset: [1.05244, 1.45583, 1.02341]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [0.493441, 4.82619, -0.866052]
Inverse:
0.99863 0.052336 8.67362e-19
-0.0511923 0.976807 -0.207912
-0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, -0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 76 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998195 -0.0563552 -0.0207622
0.0596552 0.970343 0.234254
0.006945 -0.23507 0.971954
Offset = [1.33096, 1.45269, 0.852762]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.845927 -0.0336089 -0.00248105
0.0332707 0.885344 0.231379
-0.00536406 -0.23133 0.768084
Offset = [-0.0271063, 2.09303, 5.40498]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.840936 -0.0459951 -0.0126642
0.0265431 0.879939 0.178356
-0.0208161 -0.248362 0.759439
Offset = [0.45307, 2.36213, 5.57259]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.839934 -0.0463057 -0.0100196
0.0277817 0.880257 0.173556
-0.0300558 -0.241244 0.759691
Offset = [0.3253, 2.38865, 5.42083]
Background level guess :
first place: 0 (99.9101%)
second place: 51 (0.00201513%)
Guessed background level: 0
[AtlasCreator 21:49:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:49:27] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:49:27] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG7.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG7.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG7.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
285 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 210
LowHigh Thresholds: [0,77.5625,210]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1f91a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [0.180807, 3.56972, 16.27]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-0.0493023, 0.664479, 17.1902]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999248 -0.0163136 -0.0351794
0.011358 0.990544 -0.136724
0.0370772 0.136222 0.989984
Offset = [0.745492, 2.93411, 16.8713]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 44 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.887698 -0.0205632 -0.0418817
0.0166805 0.90767 -0.0910337
0.0435739 0.090236 0.77839
Offset = [0.433768, 2.82956, 21.2266]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.887078 -0.0253055 -0.0474
0.0131862 0.905105 -0.115827
0.0391985 0.0849973 0.754604
Offset = [0.549245, 3.0749, 21.598]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.888374 -0.0216687 -0.0557251
0.0152462 0.904769 -0.115834
0.0432551 0.0817276 0.757623
Offset = [0.733495, 3.12524, 21.3888]
Guessed background level: 0
[AtlasCreator 21:53:23] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:53:26] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:53:26] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
288 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,71.3672,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xc89a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.994522 0.103956 -0.0109262
-0.104528 0.989074 -0.103956
-8.67362e-19 0.104528 0.994522
Offset: [0.199197, 1.50441, 10.6582]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [0.771443, -0.22395, 11.321]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.103956 0.989074 0.104528
-0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, -0.00273905, -0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996702 0.0810981 0.00271428
-0.0806363 0.993653 -0.0784347
-0.00905796 0.0779572 0.996916
Offset = [0.180251, 0.836271, 11.6226]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 65 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.839602 0.0705086 -0.0123284
-0.0708721 0.901088 -0.0320723
0.0100297 0.0328638 0.744781
Offset = [-0.316538, 0.686971, 17.5009]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.839698 0.0673453 -0.0241186
-0.0372753 0.896213 -0.0815525
0.00380677 0.0208803 0.725729
Offset = [-0.0593286, 1.461, 17.3311]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.837873 0.0689871 -0.0222011
-0.0374453 0.901234 -0.0890884
-0.010874 0.0244318 0.720527
Offset = [0.0143025, 1.41317, 17.5534]
Guessed background level: 0
[AtlasCreator 21:57:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.9794%)
second place: 0 (0.0251891%)
Guessed background level: 0
[AtlasCreator 21:57:28] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 21:57:28] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG9.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG9.mat --outputVolume /var/tmp/haehn/Slicer3haehn/gicZNHAtlasCreator/caseG9.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
305 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 198
LowHigh Thresholds: [0,70.8906,198]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2976,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1c59a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-1.68698, -3.82121, 13.9448]
Center: [-1.56587, 7.25499, 17.4379]
Translation: [-1.12369, -0.286948, 12.0554]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 110 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998544 0.0404252 -0.0357039
-0.0340838 0.98601 0.163162
0.0418003 -0.161708 0.985953
Offset = [-0.843129, -3.06776, 14.641]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.887943 0.00522573 -0.0530883
0.00124934 0.859081 0.121209
0.0533302 -0.121102 0.756845
Offset = [-0.808236, -0.455183, 18.502]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.885977 0.00853467 -0.0653072
0.0386577 0.856555 0.0649654
0.0419717 -0.143838 0.749945
Offset = [-0.56823, 0.0433192, 18.3257]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.883695 0.00950848 -0.0614783
0.0351041 0.857492 0.0611938
0.036967 -0.14079 0.749985
Offset = [-0.703328, 0.245142, 18.1552]
[AtlasCreator 22:01:38] Waiting for Registration to complete..
[AtlasCreator 22:01:43] DEBUG: All outputs exist!
[AtlasCreator 22:01:43] Starting iteration 4...
Warning: In /var/tmp/haehn/SLICER/TRUNK/Slicer3/Libs/MRML/vtkMRMLVolumeArchetypeStorageNode.cxx, line 478
vtkMRMLVolumeArchetypeStorageNode (0x7ff7e4a2f1a0): WriteData: removing old version of file /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Background level guess :
first place: 0 (99.6492%)
second place: 68 (0.00519283%)
Guessed background level: 0
[AtlasCreator 22:03:59] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:04:02] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:04:02] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
218 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 127
LowHigh Thresholds: [0,44.0234,127]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1bc1a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [-1.14207, 0.432173, -1.80607]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-0.858945, -1.33371, -1.14688]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 59 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998176 0.0583298 -0.0155971
-0.0594407 0.994676 -0.0841825
0.0106037 0.084956 0.996328
Offset = [-1.53763, -0.439316, -0.896101]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 64 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.953136 0.0589569 -0.0147803
-0.0595782 0.963945 -0.0458833
0.0120333 0.0466791 0.77393
Offset = [-1.55789, -0.257615, 3.35663]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.94774 0.0514694 -0.0201421
-0.0314956 0.961381 -0.0729031
0.0082727 0.0359612 0.766268
Offset = [-1.30303, 0.190549, 3.6401]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.947387 0.049229 -0.0182086
-0.0455694 0.956015 -0.0708622
0.0012197 0.0306758 0.76821
Offset = [-1.22461, -0.064471, 3.40011]
Background level guess :
first place: 0 (99.8355%)
second place: 156 (0.00356523%)
Guessed background level: 0
[AtlasCreator 22:08:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:08:33] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:08:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
269 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,64.1875,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1189a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
0.99863 0.0522642 0.00273905
-0.052336 0.997261 0.0522642
4.33681e-19 -0.052336 0.99863
Offset: [-1.11616, 0.210839, -0.723996]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-0.690072, 1.17283, -1.1249]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0522642 0.997261 -0.052336
0.00273905 0.0522642 0.99863
Singular: 0
Versor: [ -0.026168, 0.000685233, -0.026168, 0.999315 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 92 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999163 0.0232013 0.0336962
-0.0231185 0.999729 -0.00284447
-0.033753 0.00206309 0.999428
Offset = [-1.92867, 0.862141, -0.469555]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902028 0.0263516 0.0269019
-0.0269933 0.963862 0.023778
-0.0262579 -0.0244873 0.779675
Offset = [-1.82294, 0.862615, 4.05504]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.900509 0.0230003 0.0186654
-0.0304729 0.950487 -0.0237736
-0.0261459 -0.0510737 0.773253
Offset = [-1.65215, 1.63986, 4.15635]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.894896 0.0239261 0.0220184
-0.0347603 0.945727 -0.0249242
-0.0275053 -0.0488157 0.766844
Offset = [-1.69939, 1.62889, 4.20529]
Background level guess :
first place: 0 (99.1645%)
second place: 142 (0.0144934%)
Guessed background level: 0
[AtlasCreator 22:12:49] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:12:52] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:12:52] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
261 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 167
LowHigh Thresholds: [0,59.6953,167]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xbd3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.987688 -0.15622 0.00818715
0.156434 0.986335 -0.0516916
0 0.052336 0.99863
Offset: [-1.55923, 0.438287, 1.92125]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-2.52524, -0.794157, 2.27494]
Inverse:
0.987688 0.156434 0
-0.15622 0.986335 0.052336
0.00818715 -0.0516916 0.99863
Singular: 0
Versor: [ 0.0260963, 0.00205382, 0.0784322, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.993299 -0.0875784 0.075418
0.0898036 0.995603 -0.0266301
-0.0727542 0.0332245 0.996796
Offset = [-3.30635, 0.157018, 1.85319]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902034 -0.0803633 0.0930479
0.0831245 0.956805 -0.0261827
-0.0905897 0.0337186 0.766021
Offset = [-3.88563, 0.392406, 6.68149]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89769 -0.0789344 0.0879257
0.110439 0.96149 -0.0451548
-0.113732 0.027145 0.755957
Offset = [-3.72221, 0.745842, 6.69034]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.896463 -0.0831012 0.0881303
0.110611 0.965196 -0.0457387
-0.114764 0.0164552 0.757336
Offset = [-3.88099, 0.772185, 6.5985]
Background level guess :
first place: 0 (99.9963%)
second place: 141 (0.00031002%)
Guessed background level: 0
[AtlasCreator 22:16:50] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:16:54] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:16:54] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
377 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.8906,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x278fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.994522 0.102244 -0.0217327
-0.104528 0.972789 -0.206773
-1.73472e-18 0.207912 0.978148
Offset: [-1.62114, 4.1313, 4.51985]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.24988, 0.53619, 5.64229]
Inverse:
0.994522 -0.104528 -1.73472e-18
0.102244 0.972789 0.207912
-0.0217327 -0.206773 0.978148
Singular: 0
Versor: [ 0.104385, -0.0054706, -0.0520493, 0.993159 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996165 0.0746025 -0.0457155
-0.0799448 0.988408 -0.129069
0.0355567 0.132229 0.990581
Offset = [-1.14998, 2.35047, 5.42316]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898557 0.0548521 -0.0397226
-0.0574098 0.900945 -0.066401
0.0359271 0.068529 0.730758
Offset = [-1.38913, 2.09039, 10.3709]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.901428 0.0547441 -0.0472353
-0.0535019 0.899129 -0.081943
0.0333652 0.0540181 0.721711
Offset = [-1.31012, 2.13426, 10.5133]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.896644 0.0561343 -0.0450927
-0.054186 0.894367 -0.0775281
0.0414954 0.051793 0.718707
Offset = [-1.52667, 2.40931, 10.6153]
Guessed background level: 0
[AtlasCreator 22:20:41] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:20:45] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:20:45] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case19.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case19.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case19.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
331 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 220
LowHigh Thresholds: [0,81.1562,220]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2a44a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 0.104528 -1.45062e-18
-0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [4.97938, 3.4292, 1.39403]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [5.74146, 3.55243, 1.39403]
Inverse:
0.994522 -0.104528 0
0.104528 0.994522 1.38778e-17
-1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, -3.63154e-19, -0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 62 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997666 0.0680435 -0.00565816
-0.0680589 0.997678 -0.00257707
0.00546967 0.00295614 0.999981
Offset = [5.5796, 3.76189, 1.88653]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878407 0.05688 -0.000480764
-0.0568677 0.875995 0.0139935
0.00127589 -0.0139435 0.742757
Offset = [5.01308, 4.4077, 6.74646]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.880385 0.0484496 -0.0100001
-0.0478555 0.877026 -0.0304695
0.000893328 -0.0113243 0.744148
Offset = [5.29097, 4.90069, 6.48264]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.886324 0.0484922 -0.00925319
-0.0454985 0.873747 -0.0193524
-0.00202435 -0.0173911 0.741985
Offset = [5.15066, 4.50621, 6.56137]
Background level guess :
first place: 0 (99.9893%)
second place: 41 (0.00031002%)
Guessed background level: 0
[AtlasCreator 22:24:47] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:24:51] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:24:51] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
245 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 157
LowHigh Thresholds: [0,57.2812,157]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x100ca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
0.987688 0.156434 -2.17096e-18
-0.156434 0.987688 -1.37069e-17
-1.92593e-34 1.38778e-17 1
Offset: [-1.0702, -5.65287, -7.94074]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [0.0767112, -5.49809, -7.94074]
Inverse:
0.987688 -0.156434 -1.92593e-34
0.156434 0.987688 1.38778e-17
-2.17096e-18 -1.37069e-17 1
Singular: 0
Versor: [ 6.9175e-18, -5.44419e-19, -0.0784591, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 93 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997528 0.0638124 -0.0294269
-0.0634897 0.997913 0.0117729
0.0301167 -0.00987545 0.999498
Offset = [0.142632, -5.35634, -7.43997]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.915057 0.04582 -0.0599731
-0.0441443 0.87629 0.0289738
0.061217 -0.0262437 0.736748
Offset = [0.0245516, -4.70528, -1.82493]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.912093 0.0418727 -0.0697807
-0.0614638 0.878935 -0.0271582
0.0418431 -0.0570546 0.73278
Offset = [0.425778, -4.25528, -1.87528]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911472 0.0442706 -0.0686289
-0.0653139 0.880072 -0.0368305
0.0441148 -0.0503628 0.735127
Offset = [0.332744, -4.23314, -2.0242]
Background level guess :
first place: 0 (99.9754%)
second place: 87 (0.000697545%)
Guessed background level: 0
[AtlasCreator 22:29:00] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:29:04] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:29:04] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case20.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case20.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case20.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
274 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,64.5469,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x26dea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 -2.17096e-18
1.38778e-17 0.987688 0.156434
-1.92593e-34 -0.156434 0.987688
Offset: [-1.23604, -1.74642, 9.73735]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.23604, 0.859421, 8.39754]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.37069e-17 0.987688 -0.156434
-2.17096e-18 0.156434 0.987688
Singular: 0
Versor: [ -0.0784591, -5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999512 0.00646306 -0.0305633
-0.00243978 0.991526 0.129885
0.0311438 -0.129747 0.991058
Offset = [-0.699676, -1.46305, 9.41279]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.959934 0.0102803 -0.0180849
-0.0086821 0.911516 0.0863319
0.0189042 -0.0861562 0.743943
Offset = [-1.48074, -0.096524, 14.2707]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.960695 0.0111368 -0.0352208
0.034459 0.914108 0.0588267
0.0264394 -0.10114 0.743477
Offset = [-0.942505, 0.334326, 14.2785]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.963764 0.00837966 -0.0312904
0.0349048 0.90758 0.0599552
0.0180153 -0.0931195 0.742512
Offset = [-1.04542, 0.449682, 14.2475]
Guessed background level: 0
[AtlasCreator 22:32:57] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:33:01] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:33:01] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case23.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case23.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case23.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 181
LowHigh Thresholds: [0,64.5703,181]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x28f1a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.21764, -0.42024, -4.01722]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [1.21764, 3.00352, -5.89247]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999631 0.0126048 -0.0240795
-0.00758115 0.980106 0.198328
0.0261004 -0.198072 0.97984
Offset = [1.27678, -0.261469, -3.47376]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.944503 0.016747 -0.0323834
-0.0110947 0.87788 0.167438
0.0347283 -0.166968 0.706027
Offset = [1.25828, 1.2483, 1.29847]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.940512 0.00915062 -0.032927
-0.000944571 0.8795 0.10085
0.0357876 -0.182186 0.706363
Offset = [1.41679, 1.86054, 1.33591]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.943522 0.0122748 -0.0326053
-0.00333717 0.880343 0.104744
0.0362691 -0.181978 0.706532
Offset = [1.35779, 1.77749, 1.17096]
Background level guess :
first place: 0 (99.606%)
second place: 143 (0.00759549%)
Guessed background level: 0
[AtlasCreator 22:37:08] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:37:12] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:37:12] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case26.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case26.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case26.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
259 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 171
LowHigh Thresholds: [0,61.1719,171]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2060a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104385 -0.0054706
0.104528 0.993159 0.0520493
4.33681e-19 -0.052336 0.99863
Offset: [-5.39557, -2.92482, -6.23964]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-6.2338, -2.24032, -6.64054]
Inverse:
0.994522 0.104528 4.33681e-19
-0.104385 0.993159 -0.052336
-0.0054706 0.0520493 0.99863
Singular: 0
Versor: [ -0.0261411, -0.00137, 0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996508 -0.0805011 0.0221719
0.0800347 0.996567 0.0211795
-0.0238007 -0.019331 0.99953
Offset = [-6.24321, -1.87563, -6.09597]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.966982 -0.0817282 0.0131396
0.0814488 0.965106 0.0205589
-0.0147734 -0.0194182 0.781731
Offset = [-6.54293, -1.24423, -2.00429]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.964389 -0.0772113 0.00560498
0.0866275 0.959547 -0.00907587
-0.0409769 -0.0512323 0.772084
Offset = [-6.25979, -0.912535, -1.78979]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.965823 -0.07563 0.00789854
0.0827035 0.953767 -0.00978072
-0.0417673 -0.0520032 0.775986
Offset = [-6.42313, -0.706097, -1.81706]
Background level guess :
first place: 0 (99.9778%)
second place: 228 (0.00093006%)
Guessed background level: 0
[AtlasCreator 22:41:10] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:41:14] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:41:14] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
340 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 240
LowHigh Thresholds: [0,89.9062,240]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x224ca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4093
Debug: Off
Observers:
none
Matrix:
0.987688 -0.156434 2.17096e-18
0.156434 0.987688 -1.37069e-17
1.92593e-34 1.38778e-17 1
Offset: [-0.723082, 3.35483, -11.0129]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.83166, 3.02254, -11.0129]
Inverse:
0.987688 0.156434 1.92593e-34
-0.156434 0.987688 -1.51574e-35
-1.92593e-34 -1.51574e-35 1
Singular: 0
Versor: [ 6.9175e-18, 5.44419e-19, 0.0784591, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 87 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.993452 -0.113514 0.0129286
0.11287 0.992688 0.042791
-0.0176914 -0.0410516 0.999
Offset = [-1.20681, 2.45861, -10.5243]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.869189 -0.0670517 -0.000839091
0.0670348 0.89045 0.0381977
-0.00172463 -0.0381679 0.706581
Offset = [-1.95696, 3.31274, -5.74299]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.869022 -0.0637931 -0.00520222
0.052456 0.892384 0.0287524
-0.0173558 -0.0490436 0.702872
Offset = [-1.8873, 3.56601, -5.55881]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.869057 -0.0673272 -0.00179534
0.0526182 0.88675 0.0249828
-0.0157617 -0.0488963 0.705167
Offset = [-1.90638, 3.61891, -5.60651]
Guessed background level: 0
[AtlasCreator 22:45:34] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:45:38] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:45:38] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case29.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case29.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case29.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
228 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 172
LowHigh Thresholds: [0,62.9062,172]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1d09a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-7.02063, 0.935975, -6.22609]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-6.46202, 4.42664, -8.10134]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998854 0.0417223 0.0234505
-0.0456751 0.977356 0.206613
-0.0142991 -0.207448 0.978142
Offset = [-7.14979, 0.945948, -5.85109]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.888176 0.0141484 -0.0367595
-0.00821688 0.868084 0.156763
0.0385217 -0.156339 0.757662
Offset = [-6.4696, 3.33218, -2.13585]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.885641 0.0158605 -0.0268372
-0.0663402 0.871538 0.0715594
0.0441807 -0.181962 0.758779
Offset = [-6.4725, 4.09566, -2.12351]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891489 0.0239458 -0.0315109
-0.0727023 0.875106 0.069066
0.0499542 -0.1862 0.757611
Offset = [-6.59291, 3.857, -2.42089]
Background level guess :
first place: 0 (99.6932%)
second place: 135 (0.00364273%)
Guessed background level: 0
[AtlasCreator 22:49:53] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:49:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:49:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
324 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,69.3359,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2187a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-5.89261, 3.92492, -1.8792]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-5.89261, 1.14157, -0.963523]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999014 -0.0189581 -0.0401517
0.0161534 0.997482 -0.0690608
0.0413598 0.0683441 0.996804
Offset = [-5.27974, 1.19068, -0.0163587]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89427 -0.0203206 -0.0358012
0.0191086 0.948654 -0.033878
0.0364625 0.0331652 0.738925
Offset = [-5.47786, 1.6197, 4.59302]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89423 -0.0181897 -0.0408971
0.0122886 0.949248 -0.0511598
0.0262069 0.0201882 0.738025
Offset = [-5.41284, 1.76753, 4.41694]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89326 -0.0194948 -0.0408428
0.0135823 0.951199 -0.0657735
0.0242289 0.0257909 0.73897
Offset = [-5.39014, 1.66545, 4.26949]
Background level guess :
first place: 0 (99.9661%)
second place: 125 (0.00100756%)
Guessed background level: 0
[AtlasCreator 22:54:18] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:54:22] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:54:22] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case32.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case32.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case32.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
253 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 162
LowHigh Thresholds: [0,58.4531,162]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2070a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [-2.21186, -2.40675, -9.25336]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-2.21186, 1.01701, -11.1286]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999218 -0.0196667 -0.0343122
0.026654 0.975834 0.21688
0.0292176 -0.217625 0.975595
Offset = [-1.55981, -2.4462, -8.57097]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.883158 -0.0471129 -0.0644468
0.0579984 0.921662 0.179106
0.0548562 -0.182272 0.763093
Offset = [-1.24506, -1.29402, -5.14963]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877053 -0.0409901 -0.0707512
0.054892 0.908953 0.102978
0.0551795 -0.215686 0.721498
Offset = [-1.21515, -0.142701, -4.26479]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 75 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878675 -0.0370303 -0.0778978
0.0481026 0.908164 0.116257
0.0565531 -0.21727 0.730066
Offset = [-1.20355, 0.0719855, -4.40865]
Guessed background level: 0
[AtlasCreator 22:58:57] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 22:59:01] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 22:59:01] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
224 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 144
LowHigh Thresholds: [0,52.8125,144]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x15bfa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 0.0163519
-0.104528 0.982278 0.155578
1.73472e-18 -0.156434 0.987688
Offset: [4.20647, -4.24001, -13.0569]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [5.24094, -1.52521, -14.3967]
Inverse:
0.994522 -0.104528 1.73472e-18
0.103242 0.982278 -0.156434
0.0163519 0.155578 0.987688
Singular: 0
Versor: [ -0.0783516, 0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996612 0.0687227 -0.0451784
-0.0604383 0.984542 0.164389
0.0557774 -0.161102 0.98536
Offset = [5.62841, -3.89736, -11.1113]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.91663 0.0456872 -0.0375575
-0.0404874 0.880036 0.129144
0.0431121 -0.127397 0.766188
Offset = [5.25204, -2.15743, -8.45763]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911347 0.0539549 -0.0415712
-0.0623932 0.876033 0.0495783
0.0318787 -0.160329 0.756815
Offset = [5.47013, -1.4725, -8.28596]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911981 0.0490885 -0.0425408
-0.0618053 0.878172 0.0523616
0.0325197 -0.158793 0.75858
Offset = [5.34726, -1.72576, -8.42129]
Background level guess :
first place: 0 (99.8568%)
second place: 144 (0.00224764%)
Guessed background level: 0
[AtlasCreator 23:03:35] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:03:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:03:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case36.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case36.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case36.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
273 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,63,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x239ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4093
Debug: Off
Observers:
none
Matrix:
0.978148 -0.207912 2.88535e-18
0.207912 0.978148 -1.35745e-17
1.92593e-34 1.38778e-17 1
Offset: [-4.49083, 0.870913, -10.9267]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-5.95566, 0.3897, -10.9267]
Inverse:
0.978148 0.207912 1.92593e-34
-0.207912 0.978148 1.38778e-17
2.88535e-18 -1.35745e-17 1
Singular: 0
Versor: [ 6.90088e-18, 7.25312e-19, 0.104528, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 170 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.9858 -0.160852 0.0482189
0.159164 0.986558 0.0370244
-0.0535262 -0.028824 0.99815
Offset = [-5.44763, -0.607807, -11.0823]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 62 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.888004 -0.148846 0.0442711
0.143764 0.936911 0.101656
-0.0587105 -0.0940584 0.739957
Offset = [-6.21976, -0.564527, -5.06802]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.889311 -0.149359 0.0423542
0.119136 0.943312 0.0591915
-0.0832813 -0.109797 0.741862
Offset = [-6.06128, -0.401049, -5.0677]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.888649 -0.150291 0.0462869
0.121395 0.94104 0.0607552
-0.07826 -0.113167 0.739369
Offset = [-6.07655, -0.559345, -4.88749]
Background level guess :
first place: 0 (99.9645%)
second place: 127 (0.000697545%)
Guessed background level: 0
[AtlasCreator 23:08:39] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:08:43] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:08:43] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case40.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case40.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case40.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 204
LowHigh Thresholds: [0,73.7344,204]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1224a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 0.0054706
-0.052336 0.993159 0.104385
-8.67362e-19 -0.104528 0.994522
Offset: [2.37885, -2.52103, -13.3842]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [2.85044, -0.690829, -14.2321]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0520493 0.993159 -0.104528
0.0054706 0.104385 0.994522
Singular: 0
Versor: [ -0.052318, 0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999802 0.0180357 -0.00835802
-0.0169896 0.993592 0.111743
0.0103198 -0.111579 0.993702
Offset = [2.3093, -2.52974, -12.7077]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 60 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89124 0.0206994 -0.0452808
-0.0169096 0.899897 0.0825331
0.0468282 -0.081665 0.750615
Offset = [2.78285, -0.742936, -7.82666]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891557 0.0152499 -0.0581598
0.00880162 0.893234 0.0274284
0.0425477 -0.107614 0.742284
Offset = [3.14427, -0.101787, -7.84829]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891534 0.0126615 -0.051966
0.00195711 0.899466 0.0279392
0.0377486 -0.108829 0.748895
Offset = [3.1497, -0.498627, -8.09645]
Background level guess :
first place: 0 (99.8872%)
second place: 69 (0.00271267%)
Guessed background level: 0
[AtlasCreator 23:13:06] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:13:10] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:13:10] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case41.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case41.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case41.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 139
LowHigh Thresholds: [0,50.0625,139]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x147ca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 -2.17096e-18
1.38778e-17 0.987688 0.156434
-1.92593e-34 -0.156434 0.987688
Offset: [-3.22556, -1.49584, -10.0048]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-3.22556, 1.11, -11.3447]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.37069e-17 0.987688 -0.156434
-2.17096e-18 0.156434 0.987688
Singular: 0
Versor: [ -0.0784591, -5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99975 -0.0113952 0.0192593
0.00841323 0.988896 0.148372
-0.0207362 -0.148173 0.988744
Offset = [-3.6149, -1.54976, -10.6205]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.895591 -0.000800853 0.0290701
-0.00183488 0.933764 0.0905285
-0.0290232 -0.0905435 0.750159
Offset = [-4.1351, 0.278412, -5.64129]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.900428 -0.0034452 0.0162565
-0.0101569 0.913706 0.0399207
-0.0592589 -0.116424 0.745266
Offset = [-3.755, 1.05335, -5.78953]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.897078 -0.000871229 0.0140824
-0.0141191 0.919575 0.0347008
-0.0545594 -0.102835 0.742426
Offset = [-3.79367, 0.993361, -5.82311]
Guessed background level: 0
[AtlasCreator 23:17:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:17:29] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:17:29] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case42.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case42.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case42.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,70.1172,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xe28a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [-0.500266, -1.66898, -18.2481]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [0.0155393, 1.00489, -19.5879]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998916 0.0137755 -0.0444535
-0.00512126 0.981924 0.189205
0.0462563 -0.188772 0.980931
Offset = [0.778394, -2.23831, -16.8355]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 113 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.892506 0.00114998 -0.017975
0.0019305 0.901212 0.170423
0.017908 -0.17043 0.722297
Offset = [-0.207487, -0.306453, -13.2769]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.889515 -0.00215648 -0.029971
-0.0137647 0.90697 0.0964055
0.0136875 -0.184717 0.724241
Offset = [0.0053313, 0.397838, -13.5259]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.890757 0.000221978 -0.0268298
-0.0189634 0.902711 0.0997826
0.0113005 -0.181568 0.726312
Offset = [-0.0160651, 0.356971, -13.5831]
Background level guess :
first place: 0 (99.7911%)
second place: 120 (0.00356523%)
Guessed background level: 0
[AtlasCreator 23:22:04] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:22:09] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:22:09] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case46.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case46.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case46.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
226 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,54.4219,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xae0a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [4.79205, 3.45382, -1.53462]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [4.61257, -0.371239, -0.412178]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999913 -0.00602978 0.0117022
0.00791457 0.985691 -0.168378
-0.0105194 0.168456 0.985653
Offset = [3.95911, 2.07273, -1.11311]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904113 -0.0226275 0.0159258
0.0247684 0.924615 -0.150451
-0.0123353 0.150788 0.769673
Offset = [4.04255, 2.84784, 2.33675]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902622 -0.0158329 0.00772652
-0.0186158 0.922809 -0.15641
-0.0450517 0.143193 0.773731
Offset = [4.25993, 3.19974, 2.31798]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.909092 -0.0102776 0.00891055
-0.0172339 0.920895 -0.154798
-0.0489879 0.144928 0.774025
Offset = [4.18545, 3.39755, 2.21195]
Guessed background level: 0
[AtlasCreator 23:26:36] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:26:40] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:26:40] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case47.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case47.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case47.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
287 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,63.25,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e1fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [-5.78243, -0.829843, 0.304532]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-6.01192, -3.70074, 1.22021]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999547 -0.0292444 0.00713047
0.0298035 0.994727 -0.098134
-0.004223 0.098302 0.995148
Offset = [-6.02062, -1.98257, 0.767434]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.909069 -0.000302608 0.00927808
0.000818646 0.865144 -0.0556658
-0.00924685 0.055671 0.753859
Offset = [-6.76829, -1.76293, 5.82296]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908436 2.97154e-06 -0.000635666
0.0269755 0.85952 -0.0603856
-0.0188829 0.0493601 0.755539
Offset = [-6.2748, -1.71851, 5.67989]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.90985 -0.00356798 0.00044632
0.0356713 0.85941 -0.0630387
-0.0211679 0.049908 0.752101
Offset = [-6.37085, -1.41852, 5.62363]
Guessed background level: 0
[AtlasCreator 23:31:06] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:31:10] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:31:10] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case48.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case48.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case48.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
205 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 133
LowHigh Thresholds: [0,47.8047,133]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x16aaa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.994522 0.103956 -0.0109262
-0.104528 0.989074 -0.103956
-8.67362e-19 0.104528 0.994522
Offset: [0.501493, 1.13224, -11.1935]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [1.07124, -0.574446, -10.5343]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.103956 0.989074 0.104528
-0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, -0.00273905, -0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995893 0.0871286 -0.0246245
-0.0890786 0.991561 -0.0941913
0.01621 0.0959979 0.99525
Offset = [0.590232, -0.174724, -10.9201]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.935299 0.0782457 -0.0318127
-0.0787002 0.885598 -0.0132938
0.030671 0.0157499 0.737638
Offset = [0.698452, -0.153813, -4.21626]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.927244 0.0718699 -0.0458177
-0.0355705 0.884146 -0.0809091
0.0360651 -0.016129 0.735532
Offset = [0.836675, 1.14693, -4.6569]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932609 0.0691106 -0.0489095
-0.0328864 0.881718 -0.0828861
0.0300799 -0.0151831 0.734916
Offset = [1.03238, 1.23535, -4.57419]
Background level guess :
first place: 0 (99.7032%)
second place: 148 (0.00596788%)
Guessed background level: 0
[AtlasCreator 23:35:31] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:35:36] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:35:36] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,63.2109,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1191a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [1.22603, 2.16604, -16.8592]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [1.74184, 4.83991, -18.199]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 142 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998812 0.0447325 0.0193414
-0.0468419 0.990709 0.127676
-0.0134504 -0.12843 0.991627
Offset = [0.83963, 2.26146, -16.1275]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.937637 0.0348726 0.0254439
-0.0379487 0.954545 0.132606
-0.0205763 -0.133448 0.795659
Offset = [0.495121, 3.00571, -12.5172]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.936569 0.0310531 0.0173003
-0.0659468 0.947952 0.0898382
-0.0396989 -0.155575 0.791064
Offset = [0.919228, 3.56871, -12.6703]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.938738 0.0374554 0.0212613
-0.0571389 0.947354 0.0876531
-0.0420659 -0.160616 0.792718
Offset = [0.798916, 3.53304, -12.7516]
Background level guess :
first place: 0 (99.5194%)
second place: 159 (0.00658792%)
Guessed background level: 0
[AtlasCreator 23:40:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:40:30] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:40:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case51.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case51.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case51.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
265 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 174
LowHigh Thresholds: [0,63.7031,174]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1b7aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 -0.0108813
-0.052336 0.976807 -0.207627
8.67362e-19 0.207912 0.978148
Offset: [1.75273, 0.635477, 7.15782]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [1.93648, -3.02663, 8.28026]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0511923 0.976807 0.207912
-0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998961 0.0384204 0.0244991
-0.0333186 0.982651 -0.182449
-0.0310838 0.181443 0.98291
Offset = [0.873378, 0.208375, 7.14314]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.885997 0.0232177 0.0293154
-0.0190058 0.948168 -0.136564
-0.0322062 0.135912 0.765082
Offset = [0.772509, -0.610304, 12.2752]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89146 0.0251647 0.0205146
-0.0276915 0.940071 -0.140463
-0.0345025 0.125184 0.768874
Offset = [0.975331, -0.495291, 12.0958]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.885463 0.0244429 0.0179552
-0.0236126 0.941781 -0.156142
-0.0292499 0.131526 0.773728
Offset = [1.06163, -0.464542, 12.0478]
Background level guess :
first place: 0 (99.921%)
second place: 111 (0.00124008%)
Guessed background level: 0
[AtlasCreator 23:44:55] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:45:00] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:45:00] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case53.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case53.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case53.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 195
LowHigh Thresholds: [0,72.1875,195]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x22f0a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [1.46406, 2.23666, -7.02396]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [1.74719, 0.470772, -6.36477]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999103 0.0412327 0.00963241
-0.0406662 0.997765 -0.0530257
-0.0117973 0.0525864 0.998547
Offset = [1.08508, 1.41922, -5.95445]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924165 0.0366366 -0.00455441
-0.0367614 0.93588 -0.0312818
0.00340304 0.0314279 0.776625
Offset = [1.12382, 2.15956, -1.65453]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.930522 0.0291124 -0.0113882
-0.0254294 0.92566 -0.0647453
-0.0101472 0.0182817 0.776826
Offset = [1.19124, 2.67056, -1.91495]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932056 0.0357947 -0.00850299
-0.0298024 0.92488 -0.0556045
-0.0155215 0.00764992 0.770493
Offset = [1.26008, 2.5512, -1.78688]
Guessed background level: 0
[AtlasCreator 23:49:16] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:49:21] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:49:21] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case54.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case54.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case54.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
295 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 196
LowHigh Thresholds: [0,73.4062,196]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x148ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-3.48419, 1.46411, -2.28285]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-2.92558, 4.95478, -4.15811]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 91 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999253 0.0169526 0.0347291
-0.0228497 0.983916 0.177163
-0.0311671 -0.177824 0.983569
Offset = [-4.13975, 2.07938, -2.23239]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.880768 0.0100565 0.00233705
-0.0102472 0.842263 0.105672
-0.00126115 -0.105691 0.718237
Offset = [-3.60612, 4.91476, 1.90776]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.873333 0.0154402 0.000969186
-0.0280079 0.836762 0.0410263
-0.0132295 -0.127861 0.707348
Offset = [-3.6151, 5.81007, 2.08309]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 9 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.876418 0.0154782 0.0019125
-0.0291103 0.839224 0.0372637
-0.0167459 -0.125708 0.707508
Offset = [-3.6074, 5.85001, 2.24661]
Background level guess :
first place: 0 (99.8487%)
second place: 86 (0.00263517%)
Guessed background level: 0
[AtlasCreator 23:53:41] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:53:46] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:53:46] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case57.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case57.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case57.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
264 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 169
LowHigh Thresholds: [0,60.8125,169]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xbeea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [-1.61984, 1.98496, -0.0851419]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.84933, -0.885936, 0.830534]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999441 2.25623e-05 0.0334383
0.00324276 0.995221 -0.0975948
-0.0332807 0.0976486 0.994664
Offset = [-2.46053, 0.443255, 0.0216384]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 153 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.91231 -0.00611851 0.0158761
0.00718352 0.915787 -0.0679176
-0.0154235 0.0680218 0.748156
Offset = [-2.439, 1.07279, 4.76305]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.913924 -0.0114431 0.0114573
0.0160822 0.917011 -0.0847906
-0.0244903 0.0469004 0.739112
Offset = [-2.24882, 1.63812, 4.87134]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.913551 -0.01302 0.0165381
0.0208039 0.905959 -0.0947547
-0.027864 0.0541958 0.731969
Offset = [-2.41828, 1.67471, 5.07442]
Guessed background level: 0
[AtlasCreator 23:58:27] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 23:58:31] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 23:58:31] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case59.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case59.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case59.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,70.0312,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1f44a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [1.77757, 0.934419, -3.9479]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [2.0607, -0.831466, -3.28871]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 62 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998554 0.0537126 -0.00223759
-0.0537006 0.994659 -0.0881453
-0.00250887 0.088138 0.996105
Offset = [1.98526, 0.181093, -3.36361]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902505 0.0588471 0.0180965
-0.0583356 0.884448 -0.0275999
-0.0196829 0.0264919 0.747744
Offset = [0.985725, 0.185017, 2.18838]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904256 0.060555 0.00141421
-0.0415782 0.880485 -0.0626885
-0.0283644 0.0254325 0.745965
Offset = [1.22965, 0.52299, 1.97995]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.91072 0.0602919 0.0028504
-0.0378581 0.878909 -0.0643529
-0.0271987 0.0225383 0.752018
Offset = [1.24596, 0.758818, 1.73624]
Guessed background level: 0
[AtlasCreator 00:03:00] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:03:05] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:03:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case60.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case60.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case60.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
338 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 239
LowHigh Thresholds: [0,90.25,239]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e07a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.978148 0.207912 -2.88535e-18
-0.207912 0.978148 -1.35745e-17
-1.92593e-34 1.38778e-17 1
Offset: [-3.21818, 0.802985, -1.28822]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.68531, 0.969128, -1.28822]
Inverse:
0.978148 -0.207912 -1.92593e-34
0.207912 0.978148 1.38778e-17
-2.88535e-18 -1.35745e-17 1
Singular: 0
Versor: [ 6.90088e-18, -7.25312e-19, -0.104528, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.984565 0.172745 -0.0281396
-0.173319 0.984674 -0.0194303
0.0243519 0.0240076 0.999415
Offset = [-2.34541, 0.77382, -1.02675]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877575 0.0325775 -0.0540348
-0.0296203 0.889747 0.054654
0.0557108 -0.0529445 0.702819
Offset = [-1.82525, 1.0351, 5.16148]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877107 0.0300521 -0.0663681
-0.0246184 0.88568 0.00703017
0.0529001 -0.0811425 0.693516
Offset = [-1.42305, 1.71729, 5.24703]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877673 0.0303907 -0.0605634
-0.0281288 0.887546 0.00252424
0.0516132 -0.0744521 0.698727
Offset = [-1.5239, 1.77987, 5.06325]
Background level guess :
first place: 0 (99.929%)
second place: 112 (0.00186012%)
Guessed background level: 0
[AtlasCreator 00:07:23] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:07:27] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:07:27] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case61.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case61.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case61.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,53.9062,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x26bda50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.994522 -0.102244 0.0217327
0.104528 0.972789 -0.206773
1.73472e-18 0.207912 0.978148
Offset: [-1.13505, -0.585518, 4.44157]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.48926, -4.50609, 5.56401]
Inverse:
0.994522 0.104528 1.73472e-18
-0.102244 0.972789 0.207912
0.0217327 -0.206773 0.978148
Singular: 0
Versor: [ 0.104385, 0.0054706, 0.0520493, 0.993159 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997251 -0.0211724 0.0710031
0.0397464 0.961617 -0.271501
-0.0625295 0.273577 0.959816
Offset = [-2.80167, -0.30902, 5.08901]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 71 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.937721 -0.0180644 0.0571185
0.0302916 0.882414 -0.221091
-0.0516843 0.222424 0.739597
Offset = [-2.61027, -0.136004, 8.83867]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93895 -0.0226462 0.0441327
0.0532657 0.879884 -0.228288
-0.0738958 0.211392 0.737075
Offset = [-2.22431, 0.138979, 9.06275]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.940528 -0.0205312 0.0444732
0.0561421 0.877417 -0.234922
-0.0764136 0.21758 0.73878
Offset = [-2.12037, 0.317984, 8.99981]
Background level guess :
first place: 0 (99.9685%)
second place: 147 (0.000852555%)
Guessed background level: 0
[AtlasCreator 00:11:55] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:11:59] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:11:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case62.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case62.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case62.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
252 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,62.1562,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x130aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-3.49747, 7.22929, -1.32556]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-3.49747, 4.44594, -0.409886]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999893 -0.0129538 -0.00675535
0.0121949 0.994677 -0.10232
0.00804482 0.102227 0.994729
Offset = [-3.50076, 5.74008, -1.1334]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.918027 -0.022375 -0.00506239
0.0225154 0.87681 0.02963
0.00439592 -0.0297362 0.717074
Offset = [-3.80843, 4.05887, 6.39989]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.913938 -0.0254841 -0.0130928
0.0174998 0.873405 -0.0378062
-0.0167976 -0.0377549 0.722213
Offset = [-3.43409, 5.69669, 5.88318]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.916901 -0.0238602 -0.0189963
0.0118951 0.871773 -0.0352084
-0.0170408 -0.0405197 0.729398
Offset = [-3.38085, 5.51986, 5.4519]
Background level guess :
first place: 0 (99.5161%)
second place: 137 (0.00713046%)
Guessed background level: 0
[AtlasCreator 00:16:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:16:29] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:16:29] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/case8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
263 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 160
LowHigh Thresholds: [0,58.2422,160]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xc1ca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [0.483832, -1.03818, 7.32973]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [0.204971, -2.96701, 7.98892]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 107 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999532 -0.0233976 -0.0197299
0.0221411 0.997852 -0.0616599
0.0211302 0.0611942 0.997902
Offset = [0.174482, -1.19272, 8.47666]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.831607 -0.0318073 -0.0231804
0.0310308 0.960875 -0.0331193
0.0242099 0.0323744 0.734171
Offset = [-0.0136877, -1.41233, 12.7156]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.832359 -0.0238932 -0.0275145
0.000154518 0.955916 -0.0701028
0.000838863 0.0299174 0.735784
Offset = [0.239575, -0.837888, 12.555]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.836165 -0.0255942 -0.020835
0.0160692 0.9598 -0.07461
0.00241192 0.0337839 0.736788
Offset = [0.199086, -0.873792, 12.5837]
Background level guess :
first place: 0 (99.7564%)
second place: 38 (0.00302269%)
Guessed background level: 0
[AtlasCreator 00:21:19] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:21:25] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:21:25] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG1.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG1.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG1.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
347 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 234
LowHigh Thresholds: [0,86.4844,234]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2962a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4057
Debug: Off
Observers:
none
Matrix:
0.994522 0.104528 -1.45062e-18
-0.104528 0.994522 -1.38018e-17
0 1.38778e-17 1
Offset: [0.755198, -2.67048, 5.34399]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [1.51728, -2.54724, 5.34399]
Inverse:
0.994522 -0.104528 0
0.104528 0.994522 1.38778e-17
-1.45062e-18 -1.38018e-17 1
Singular: 0
Versor: [ 6.92938e-18, -3.63154e-19, -0.052336, 0.99863 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 96 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995672 0.0601599 -0.0708449
-0.0597908 0.998184 0.00732033
0.0711566 -0.00305277 0.99746
Offset = [2.16971, -2.31738, 5.52965]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.895145 0.0505623 -0.0725022
-0.0501398 0.939759 0.00763692
0.0727951 -0.00397178 0.780913
Offset = [1.9476, -1.60334, 9.54999]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89303 0.0513606 -0.0824197
-0.0261583 0.942197 0.00480468
0.0749044 -0.00379413 0.784987
Offset = [2.18594, -1.57135, 9.58529]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.890145 0.0521074 -0.0782003
-0.0277386 0.938577 -0.0012075
0.0693717 0.00493974 0.776312
Offset = [2.11245, -1.32331, 9.81159]
Background level guess :
first place: 0 (99.7627%)
second place: 186 (0.00410776%)
Guessed background level: 0
[AtlasCreator 00:26:04] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:26:08] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:26:08] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 215
LowHigh Thresholds: [0,80.8828,215]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xe8ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [3.51448, 3.61076, 15.9438]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [3.28499, 0.739867, 16.8595]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 92 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997658 -0.060313 -0.0322548
0.0582932 0.996479 -0.0602673
0.0357762 0.0582459 0.997661
Offset = [4.55904, 1.81177, 16.9489]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.882613 -0.059974 -0.0223168
0.058302 0.929915 -0.0692432
0.026378 0.0678002 0.753312
Offset = [3.46003, 2.64122, 21.9068]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.886742 -0.056511 -0.0213649
0.0477309 0.923073 -0.118011
-8.43576e-05 0.0473713 0.747601
Offset = [3.6083, 3.28204, 21.792]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.886085 -0.0577293 -0.0263345
0.046416 0.922628 -0.126064
0.00305197 0.0509033 0.744989
Offset = [3.69805, 3.35455, 21.6119]
Background level guess :
first place: 0 (99.8225%)
second place: 6 (0.00767299%)
Guessed background level: 0
[AtlasCreator 00:30:35] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:30:40] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:30:40] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG11.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG11.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG11.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.7344,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1ad3a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4051
Debug: Off
Observers:
none
Matrix:
1 0 0
0 1 0
0 0 1
Offset: [3.45713, -2.39959, 9.82973]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [3.45713, -2.39959, 9.82973]
Inverse:
1 0 0
0 1 0
0 0 1
Singular: 0
Versor: [ 0, 0, 0, 1 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 47 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999571 0.0144984 0.0254417
-0.0146991 0.999862 0.00771759
-0.0253263 -0.00808825 0.999647
Offset = [2.7013, -1.9438, 9.5276]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877507 0.0146118 0.0234018
-0.013736 0.909461 -0.0371561
-0.0239263 0.0368205 0.750382
Offset = [2.36883, -0.681746, 14.5298]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877376 0.00640018 0.0145634
-0.00424164 0.912051 -0.0614674
-0.0466321 0.0274841 0.743892
Offset = [2.54441, -0.507689, 14.2397]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.882621 0.0137294 0.00649551
-0.0128166 0.911163 -0.0630678
-0.0478496 0.0295514 0.74939
Offset = [2.83753, -0.674156, 14.1716]
Guessed background level: 0
[AtlasCreator 00:35:00] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:35:05] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:35:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
321 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.5,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1dbba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-1.38298, 2.35618, 0.480445]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.38298, -0.427176, 1.39612]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 9 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999825 -0.0123514 -0.0140586
0.010473 0.991896 -0.126618
0.0155086 0.126449 0.991852
Offset = [-0.823617, 1.80462, 0.805401]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.858187 -0.0157607 0.0175124
0.0160169 0.87593 -0.0145885
-0.0172784 0.0148649 0.714739
Offset = [-2.21766, 0.956173, 7.42483]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.854708 -0.00559804 0.0124024
-0.0119898 0.872222 -0.0638796
-0.0513843 -0.0100683 0.705714
Offset = [-2.00626, 1.58588, 7.27543]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.861921 -0.00271488 0.0108733
-0.014982 0.871749 -0.0609086
-0.0522571 -0.0108739 0.708033
Offset = [-1.85874, 1.63343, 7.13305]
Background level guess :
first place: 0 (99.7555%)
second place: 81 (0.00325521%)
Guessed background level: 0
[AtlasCreator 00:39:15] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:39:19] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:39:19] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG13.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG13.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG13.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.0938,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x245fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [-1.02045, 0.947635, 11.6333]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.29931, -0.981203, 12.2924]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998673 -0.0382918 0.0344417
0.0401822 0.997623 -0.0559818
-0.0322162 0.0572914 0.997838
Offset = [-1.15421, -0.485778, 12.1511]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920536 -0.0199589 0.0395757
0.0210899 0.928498 -0.0283702
-0.0389847 0.029177 0.759275
Offset = [-1.96403, -0.201257, 16.992]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.923604 -0.0153436 0.0344404
0.02899 0.933631 -0.0635593
-0.0682671 0.0235319 0.762607
Offset = [-1.92114, 0.282637, 16.7442]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.91827 -0.0151246 0.0331829
0.0315107 0.930644 -0.0699905
-0.0569284 0.0220664 0.761273
Offset = [-1.96466, 0.25837, 16.7898]
Background level guess :
first place: 0 (98.828%)
second place: 187 (0.0134859%)
Guessed background level: 0
[AtlasCreator 00:43:32] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:43:37] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:43:37] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
348 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,80.2812,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xe06a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.14567, 3.21827, 12.918]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [3.14567, -0.520557, 14.0404]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 60 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99997 -0.00206297 0.00748574
0.00361447 0.976913 -0.213608
-0.00687225 0.213628 0.976891
Offset = [2.45503, 3.24898, 13.944]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.934286 0.00377879 0.0103123
-0.00172852 0.951969 -0.192009
-0.010846 0.191979 0.813286
Offset = [2.48176, 2.62234, 17.3441]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.930013 -0.00355746 0.0040438
0.00773553 0.957713 -0.192687
-0.0407098 0.193564 0.80956
Offset = [2.61864, 2.59007, 17.5096]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932089 -0.00311494 -0.00345611
0.0178201 0.948885 -0.195613
-0.0406255 0.190758 0.809004
Offset = [2.71724, 2.69183, 17.3071]
Background level guess :
first place: 0 (99.838%)
second place: 81 (0.00387525%)
Guessed background level: 0
[AtlasCreator 00:47:32] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:47:37] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:47:37] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 186
LowHigh Thresholds: [0,69.8438,186]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x17a7a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 -0.00818715
0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [0.680284, -4.06052, -2.73093]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [0.168745, -1.54961, -4.07074]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 -0.156434
-0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, -0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998082 -0.0588738 -0.0191453
0.0609448 0.988734 0.136713
0.0108808 -0.137617 0.990426
Offset = [0.531327, -2.25941, -3.19009]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.910451 -0.045415 -0.0226518
0.047662 0.924567 0.111219
0.0174344 -0.112155 0.788249
Offset = [0.498068, -2.25972, 1.60818]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 47 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921583 -0.0435092 -0.0300756
0.103984 0.924766 0.0383725
0.00556459 -0.14874 0.783956
Offset = [0.536754, -1.27589, 1.47617]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924208 -0.0436732 -0.0265922
0.103414 0.924212 0.0351459
0.00612765 -0.149173 0.782444
Offset = [0.778446, -1.25721, 1.45624]
Guessed background level: 0
[AtlasCreator 00:51:52] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:51:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:51:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG16.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG16.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG16.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 225
LowHigh Thresholds: [0,84.6094,225]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x15b0a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-1.7749, 3.30232, -5.014]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.95438, -0.522741, -3.89156]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999121 -0.0381283 -0.0174268
0.0349152 0.986903 -0.157488
0.0232033 0.156741 0.987367
Offset = [-1.40057, 2.02769, -4.81714]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.855723 -0.0256569 -0.0291739
0.0247138 0.853782 -0.0322399
0.029977 0.0314945 0.70896
Offset = [-1.94421, 1.00365, 2.39498]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.866601 -0.0229403 -0.0431696
0.0453825 0.850936 -0.0797238
0.0198379 0.0171871 0.697855
Offset = [-1.59614, 1.69011, 2.12407]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.860396 -0.0220721 -0.0434889
0.0464225 0.855794 -0.0878647
0.018674 0.0176466 0.703572
Offset = [-1.5011, 1.83648, 1.82356]
Background level guess :
first place: 0 (99.6543%)
second place: 214 (0.00496032%)
Guessed background level: 0
[AtlasCreator 00:55:51] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 00:55:55] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 00:55:55] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG17.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG17.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG17.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
373 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 246
LowHigh Thresholds: [0,90.8516,246]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2489a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 -0.0108813
-0.052336 0.976807 -0.207627
8.67362e-19 0.207912 0.978148
Offset: [4.88866, 3.62418, 13.5347]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [5.07242, -0.037931, 14.6571]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0511923 0.976807 0.207912
-0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999358 0.034385 0.0100857
-0.0326013 0.989276 -0.142371
-0.0148729 0.141951 0.989762
Offset = [4.19466, 2.79359, 14.1333]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 55 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905993 0.0484556 0.0188522
-0.0458499 0.939702 -0.120161
-0.0245181 0.119134 0.766714
Offset = [3.95747, 3.14933, 18.3942]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905406 0.044261 -0.00936029
-0.0336048 0.926619 -0.162546
-0.0475213 0.107924 0.757051
Offset = [4.44735, 3.8385, 18.6184]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904349 0.042365 -0.00962671
-0.037596 0.930169 -0.16361
-0.0390695 0.114338 0.756305
Offset = [4.35633, 3.71026, 18.4889]
Guessed background level: 0
[AtlasCreator 01:00:03] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:00:08] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:00:08] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
280 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 201
LowHigh Thresholds: [0,73.75,201]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1622a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 0.0163519
-0.104528 0.982278 0.155578
1.73472e-18 -0.156434 0.987688
Offset: [3.80921, -2.87301, -1.90001]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [4.84368, -0.158206, -3.23983]
Inverse:
0.994522 -0.104528 1.73472e-18
0.103242 0.982278 -0.156434
0.0163519 0.155578 0.987688
Singular: 0
Versor: [ -0.0783516, 0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.993732 0.0916238 -0.0640403
-0.0818597 0.98658 0.141278
0.0761253 -0.13515 0.987896
Offset = [4.84339, -3.35802, -2.29569]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93115 0.0729247 -0.0694428
-0.064189 0.875106 0.120644
0.0775893 -0.115574 0.769006
Offset = [4.9014, -1.542, 2.95301]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93526 0.0817821 -0.0731177
-0.0140248 0.884176 0.0699452
0.0568792 -0.133352 0.774073
Offset = [5.05505, -0.790094, 2.78794]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93721 0.0825644 -0.073248
-0.00916052 0.884459 0.0677566
0.0549952 -0.135026 0.762761
Offset = [5.09153, -0.776495, 2.92927]
Guessed background level: 0
[AtlasCreator 01:04:09] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:04:14] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:04:14] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
266 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2812,177]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1176a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.75842, -3.01847, -0.489809]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [1.75842, 0.405289, -2.36507]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999999 0.00100435 0.00105733
-0.00120608 0.977165 0.212478
-0.000819781 -0.212479 0.977165
Offset = [1.60855, -3.19945, -0.667093]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.936361 -0.00346228 0.0046985
0.00271636 0.900648 0.150385
-0.00516572 -0.15037 0.758106
Offset = [1.48188, -1.3167, 3.68953]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.933645 -0.00934101 -0.0167685
0.000587847 0.893117 0.0733685
-0.00673501 -0.172676 0.749627
Offset = [1.98929, -0.26257, 3.6543]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.935676 -0.00849955 -0.0100609
0.000336472 0.891319 0.0719008
-0.00917143 -0.177102 0.750545
Offset = [2.07157, -0.251953, 3.47471]
Background level guess :
first place: 0 (99.81%)
second place: 65 (0.00279018%)
Guessed background level: 0
[AtlasCreator 01:08:15] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:08:20] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:08:20] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
294 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,69.1875,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x204ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [4.082, 3.26808, 15.0461]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [3.80314, 1.33924, 15.7053]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998852 -0.0403104 -0.0258664
0.0378655 0.99532 -0.0889059
0.0293292 0.0878244 0.995704
Offset = [4.71154, 2.40852, 14.9878]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.889951 -0.0305911 -0.0130969
0.0301122 0.919405 -0.0353182
0.0141632 0.0349043 0.762282
Offset = [4.12928, 2.37496, 19.4122]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891797 -0.0197587 -0.0161223
0.0544017 0.915521 -0.042168
-0.0147213 0.0159647 0.749945
Offset = [4.12366, 2.61629, 19.8265]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.895863 -0.028761 -0.0213854
0.0615754 0.915177 -0.0489295
-0.00723826 0.0246002 0.748693
Offset = [4.39349, 2.61944, 19.7699]
Background level guess :
first place: 0 (99.9727%)
second place: 101 (0.0016276%)
Guessed background level: 0
[AtlasCreator 01:12:13] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:12:18] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:12:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 227
LowHigh Thresholds: [0,84.7656,227]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xf37a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.987688 -0.15622 -0.00818715
0.156434 0.986335 0.0516916
8.67362e-19 -0.052336 0.99863
Offset: [-1.49213, 2.12019, 9.28176]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-2.74018, 2.66854, 8.88086]
Inverse:
0.987688 0.156434 8.67362e-19
-0.15622 0.986335 -0.052336
-0.00818715 0.0516916 0.99863
Singular: 0
Versor: [ -0.0260963, -0.00205382, 0.0784322, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.989137 -0.142361 0.0366144
0.140196 0.988531 0.0561371
-0.0441862 -0.0503941 0.997751
Offset = [-2.50012, 1.65497, 9.12942]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.88677 -0.118522 0.0277029
0.117411 0.898568 0.0387952
-0.0320884 -0.0352541 0.792942
Offset = [-3.01537, 3.4957, 13.6969]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.889151 -0.12402 0.0300748
0.103833 0.891266 -0.0215092
-0.0580281 -0.0666108 0.791545
Offset = [-2.88092, 3.87058, 13.4047]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.887418 -0.122441 0.026674
0.0976631 0.891852 -0.0268641
-0.0513318 -0.0689139 0.793204
Offset = [-3.01329, 4.05526, 13.3969]
Background level guess :
first place: 0 (99.8485%)
second place: 76 (0.00217014%)
Guessed background level: 0
[AtlasCreator 01:16:15] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:16:20] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:16:20] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG4.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG4.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG4.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 205
LowHigh Thresholds: [0,75.9375,205]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xbdca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.994522 0.102244 -0.0217327
-0.104528 0.972789 -0.206773
-1.73472e-18 0.207912 0.978148
Offset: [0.584383, 1.78855, 17.6506]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [0.955648, -1.80656, 18.7731]
Inverse:
0.994522 -0.104528 -1.73472e-18
0.102244 0.972789 0.207912
-0.0217327 -0.206773 0.978148
Singular: 0
Versor: [ 0.104385, -0.0054706, -0.0520493, 0.993159 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998178 0.0303316 -0.0521508
-0.0408242 0.976045 -0.213703
0.0444196 0.215443 0.975506
Offset = [1.74521, 1.53995, 17.5931]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 54 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.823912 -0.000821386 -0.0394056
-0.00357235 0.929989 -0.1113
0.039252 0.111354 0.689552
Offset = [0.697081, 0.853864, 24.4463]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.82088 0.00766982 -0.0349764
0.00760275 0.926436 -0.134524
0.0265756 0.105814 0.684335
Offset = [0.690531, 0.993399, 24.5268]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.820072 0.00276724 -0.0361543
0.00841003 0.924053 -0.129848
0.0288607 0.105752 0.690845
Offset = [0.8031, 0.686388, 24.3439]
Background level guess :
first place: 0 (99.959%)
second place: 76 (0.00139509%)
Guessed background level: 0
[AtlasCreator 01:20:25] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:20:30] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:20:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,82.5,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1579a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.42538, 6.0952, 5.01596]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [3.42538, 2.35637, 6.1384]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 118 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999469 -0.0302726 0.0120789
0.0319455 0.983372 -0.178769
-0.00646628 0.17906 0.983817
Offset = [2.96467, 5.35996, 6.09934]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 55 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908209 -0.0233114 -0.00142332
0.0230433 0.879542 -0.102367
0.00380179 0.102307 0.719467
Offset = [3.00601, 5.42426, 11.0089]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905488 -0.025681 -0.00111001
0.0293112 0.879194 -0.135239
-0.0106261 0.0927878 0.720284
Offset = [3.08738, 5.88665, 10.5895]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907554 -0.0202039 -0.00151331
0.0247347 0.88222 -0.134617
-0.0098065 0.092287 0.728291
Offset = [3.00909, 6.03108, 10.5899]
Background level guess :
first place: 0 (99.998%)
second place: 84 (0.00031002%)
Guessed background level: 0
[AtlasCreator 01:24:51] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:24:56] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:24:56] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG6.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG6.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG6.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
286 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 209
LowHigh Thresholds: [0,77.25,209]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1648a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 -0.0108813
0.052336 0.976807 0.207627
8.67362e-19 -0.207912 0.978148
Offset: [1.03873, 1.54441, 1.22203]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [0.484383, 4.87212, -0.653225]
Inverse:
0.99863 0.052336 8.67362e-19
-0.0511923 0.976807 -0.207912
-0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, -0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999041 -0.0310049 -0.0309303
0.0370987 0.974462 0.221468
0.0232738 -0.222403 0.974677
Offset = [1.42357, 0.877707, 1.42403]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 51 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.836618 -0.0393004 -0.00515553
0.0394476 0.873022 0.226196
-0.0038718 -0.226221 0.742492
Offset = [0.104163, 2.34588, 5.88971]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.831855 -0.0421305 -0.0166066
0.0267037 0.870641 0.174494
-0.0233563 -0.243755 0.748037
Offset = [0.51188, 2.76465, 5.7328]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.834282 -0.0361927 -0.0110298
0.0214753 0.866905 0.168407
-0.022608 -0.244826 0.741505
Offset = [0.356987, 2.85858, 6.29159]
Background level guess :
first place: 0 (99.9101%)
second place: 51 (0.00201513%)
Guessed background level: 0
[AtlasCreator 01:29:00] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:29:05] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:29:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG7.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG7.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG7.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
285 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 210
LowHigh Thresholds: [0,77.5625,210]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1693a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [0.121123, 4.53548, 16.2806]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-0.0583607, 0.710413, 17.4031]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999288 -0.035811 -0.0118565
0.0333968 0.986003 -0.163346
0.0175402 0.162834 0.986498
Offset = [0.230773, 3.52601, 17.0484]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.880892 -0.0247623 -0.0442647
0.0208281 0.89434 -0.0872321
0.0462464 0.0861979 0.740901
Offset = [0.343982, 2.82856, 22.1]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.880801 -0.030371 -0.0494844
0.0157403 0.899202 -0.103368
0.0410088 0.0818885 0.740842
Offset = [0.541422, 3.12017, 22.0834]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.88417 -0.0222877 -0.0508298
0.0166222 0.895131 -0.107478
0.0401001 0.0728092 0.74169
Offset = [0.668928, 3.17495, 21.9246]
Guessed background level: 0
[AtlasCreator 01:32:59] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:33:04] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:33:04] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
288 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,71.3672,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1743a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.994522 0.103956 -0.0109262
-0.104528 0.989074 -0.103956
-8.67362e-19 0.104528 0.994522
Offset: [0.192638, 1.52867, 10.8746]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [0.762385, -0.178016, 11.5338]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.103956 0.989074 0.104528
-0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, -0.00273905, -0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996939 0.0778114 0.00756329
-0.0770962 0.99457 -0.0699008
-0.0129613 0.0691038 0.997525
Offset = [-0.0819051, 0.749675, 11.3772]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 66 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.829973 0.0697243 -0.0150189
-0.0701712 0.891781 -0.0316267
0.0127692 0.0326001 0.714286
Offset = [-0.364837, 0.6975, 18.2604]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.831009 0.0663004 -0.0296921
-0.0307081 0.885835 -0.0844319
0.000380968 0.0191567 0.707275
Offset = [0.143483, 1.60218, 17.9747]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.83235 0.067177 -0.0274044
-0.0344679 0.886933 -0.0802813
-0.00538112 0.0165512 0.709127
Offset = [-0.0508734, 1.43791, 17.9953]
Guessed background level: 0
[AtlasCreator 01:37:04] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.5208%)
second place: 0 (0.0277468%)
Guessed background level: 0
[AtlasCreator 01:37:09] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:37:09] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG9.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG9.mat --outputVolume /var/tmp/haehn/Slicer3haehn/ND_xeYAtlasCreator/caseG9.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
305 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 198
LowHigh Thresholds: [0,70.8906,198]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.3328,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2a1ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-1.69136, -3.73168, 14.1435]
Center: [-1.55681, 7.20906, 17.2251]
Translation: [-1.13274, -0.241014, 12.2682]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997911 0.0342657 -0.0547663
-0.0283778 0.994079 0.104888
0.0580361 -0.103115 0.992975
Offset = [-0.221525, -1.58699, 13.6886]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878039 0.00684906 -0.0583973
-8.6813e-05 0.844267 0.115021
0.0587975 -0.114817 0.727277
Offset = [-0.825025, -0.289733, 19.2407]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.876449 0.00988566 -0.0608183
0.0362849 0.845747 0.066385
0.0389907 -0.152361 0.739245
Offset = [-0.728551, 0.322837, 18.6518]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.875267 0.0132155 -0.0595542
0.0254944 0.849705 0.0675546
0.0408517 -0.153977 0.737527
Offset = [-0.73272, 0.355608, 18.5311]
[AtlasCreator 01:41:03] Waiting for Registration to complete..
[AtlasCreator 01:41:08] DEBUG: All outputs exist!
[AtlasCreator 01:41:08] Starting iteration 5...
Warning: In /var/tmp/haehn/SLICER/TRUNK/Slicer3/Libs/MRML/vtkMRMLVolumeArchetypeStorageNode.cxx, line 478
vtkMRMLVolumeArchetypeStorageNode (0x7ff6cd520c30): WriteData: removing old version of file /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Background level guess :
first place: 0 (99.6492%)
second place: 68 (0.00519283%)
Guessed background level: 0
[AtlasCreator 01:45:35] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 01:45:41] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:45:41] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
218 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 127
LowHigh Thresholds: [0,44.0234,127]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2871a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [-1.1244, 0.393037, -1.65851]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-0.839251, -1.35624, -0.996141]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998651 0.0492605 -0.0164
-0.0502116 0.9967 -0.0637803
0.013204 0.0645178 0.997829
Offset = [-1.45959, -0.817875, -0.45341]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.935063 0.0527003 -0.0100368
-0.0531104 0.947905 -0.0462799
0.00757289 0.0467463 0.760637
Offset = [-1.39809, 0.0267817, 3.87606]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.944629 0.0485374 -0.021481
-0.0323998 0.942394 -0.0816889
0.00681877 0.029656 0.758947
Offset = [-1.16594, 0.264151, 3.78263]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 96 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.942581 0.0502858 -0.0202543
-0.0397562 0.949129 -0.0718684
0.00752236 0.0289855 0.761966
Offset = [-1.423, -0.0393789, 3.48738]
Background level guess :
first place: 0 (99.8355%)
second place: 156 (0.00356523%)
Guessed background level: 0
[AtlasCreator 01:50:06] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 01:50:12] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:50:12] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
269 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,64.1875,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1b82a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4060
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 0.0054706
-0.052336 0.993159 0.104385
-8.67362e-19 -0.104528 0.994522
Offset: [-1.14234, -0.665043, -0.124712]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-0.670378, 1.1503, -0.974153]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0520493 0.993159 -0.104528
0.0054706 0.104385 0.994522
Singular: 0
Versor: [ -0.052318, 0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998232 0.0330568 0.049393
-0.0351918 0.998455 0.0429995
-0.0478952 -0.0446617 0.997853
Offset = [-2.13954, 0.298403, -0.49544]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 71 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.888736 0.023715 0.0249053
-0.0245853 0.94978 0.0352379
-0.0240466 -0.0358293 0.768787
Offset = [-1.71455, 1.14358, 4.40253]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.893718 0.0204666 0.0205882
-0.0276797 0.936514 -0.023208
-0.0255626 -0.0577446 0.752653
Offset = [-1.55568, 1.78498, 4.80075]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.893901 0.0233521 0.0235157
-0.0361977 0.939007 -0.0191268
-0.0330257 -0.0546243 0.753786
Offset = [-1.61646, 1.70555, 4.53841]
Background level guess :
first place: 0 (99.1645%)
second place: 142 (0.0144934%)
Guessed background level: 0
[AtlasCreator 01:54:18] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 01:54:25] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:54:25] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
261 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 167
LowHigh Thresholds: [0,59.6953,167]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x23dfa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.987688 -0.15622 0.00818715
0.156434 0.986335 -0.0516916
0 0.052336 0.99863
Offset: [-1.53502, 0.411359, 2.07061]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-2.50554, -0.816682, 2.42568]
Inverse:
0.987688 0.156434 0
-0.15622 0.986335 0.052336
0.00818715 -0.0516916 0.99863
Singular: 0
Versor: [ 0.0260963, 0.00205382, 0.0784322, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.989661 -0.103827 0.0989472
0.110833 0.991501 -0.0681368
-0.0910317 0.0783989 0.992757
Offset = [-3.5859, 1.02865, 1.98202]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.890648 -0.0813321 0.0952515
0.0834089 0.950307 -0.0180228
-0.0934383 0.0258258 0.748786
Offset = [-3.90643, 0.377712, 6.96621]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.888314 -0.0827085 0.0909985
0.117702 0.952562 -0.039538
-0.118208 0.00970628 0.745142
Offset = [-3.84007, 0.893645, 6.97726]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89052 -0.0730375 0.0846401
0.104084 0.950951 -0.0393446
-0.112776 0.0127001 0.750605
Offset = [-3.87939, 0.717132, 6.8822]
Background level guess :
first place: 0 (99.9963%)
second place: 141 (0.00031002%)
Guessed background level: 0
[AtlasCreator 01:58:33] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 01:58:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 01:58:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
377 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.8906,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x28aaa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.994522 0.102244 -0.0217327
-0.104528 0.972789 -0.206773
-1.73472e-18 0.207912 0.978148
Offset: [-1.60714, 4.07616, 4.66261]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.23018, 0.513666, 5.79303]
Inverse:
0.994522 -0.104528 -1.73472e-18
0.102244 0.972789 0.207912
-0.0217327 -0.206773 0.978148
Singular: 0
Versor: [ 0.104385, -0.0054706, -0.0520493, 0.993159 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 59 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995949 0.0601053 -0.0668842
-0.0660539 0.993694 -0.0906053
0.0610166 0.0946562 0.993638
Offset = [-1.14451, 0.965708, 6.8186]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891119 0.0556055 -0.0373677
-0.0578874 0.881679 -0.0630462
0.0337249 0.0650677 0.707428
Offset = [-1.52645, 2.10169, 11.0154]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.891764 0.0549676 -0.0410005
-0.051896 0.88439 -0.0847227
0.0311774 0.0563562 0.708339
Offset = [-1.38722, 2.29845, 10.9906]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.889508 0.0558484 -0.0430968
-0.0487242 0.881016 -0.079909
0.0399666 0.0545333 0.71035
Offset = [-1.409, 2.61089, 11.0039]
Guessed background level: 0
[AtlasCreator 02:02:41] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:02:47] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:02:47] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case19.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case19.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case19.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
331 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 220
LowHigh Thresholds: [0,81.1562,220]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1a28a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 -0.00818715
-0.052336 0.986335 -0.15622
8.67362e-19 0.156434 0.987688
Offset: [5.52497, 6.21358, 0.623714]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [5.76115, 3.52991, 1.54477]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0516916 0.986335 0.156434
-0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, -0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99678 0.0801299 -0.00312528
-0.0799692 0.990374 -0.11298
-0.00595788 0.112866 0.993592
Offset = [5.42297, 5.13107, 0.63998]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.876851 0.0506912 -0.00264778
-0.0506582 0.869376 0.0113221
0.00321814 -0.0111734 0.731836
Offset = [4.94386, 4.52009, 6.86487]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.876611 0.0489277 -0.00392067
-0.0465478 0.867385 -0.0199853
-0.000925406 -0.0226772 0.732567
Offset = [5.12795, 4.82761, 6.81294]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.873539 0.0481715 -0.00386458
-0.0485588 0.862651 -0.0206268
-0.000622833 -0.0219878 0.728012
Offset = [5.05441, 4.97753, 6.74604]
Background level guess :
first place: 0 (99.9893%)
second place: 41 (0.00031002%)
Guessed background level: 0
[AtlasCreator 02:06:40] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:06:47] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:06:47] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
245 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 157
LowHigh Thresholds: [0,57.2812,157]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2435a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.987688 0.156434 -2.17096e-18
-0.156434 0.987688 -1.37069e-17
-1.92593e-34 1.38778e-17 1
Offset: [-1.05427, -5.6782, -7.79]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [0.0964048, -5.52061, -7.79]
Inverse:
0.987688 -0.156434 -1.92593e-34
0.156434 0.987688 1.38778e-17
-2.17096e-18 -1.37069e-17 1
Singular: 0
Versor: [ 6.9175e-18, -5.44419e-19, -0.0784591, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 74 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.994182 0.107051 -0.0118923
-0.107212 0.994139 -0.0138724
0.0103375 0.0150667 0.999833
Offset = [-0.52558, -5.25665, -7.49515]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.910649 0.041251 -0.0595503
-0.0392879 0.872793 0.0337677
0.0608633 -0.0313394 0.730301
Offset = [0.0745705, -4.79314, -1.48715]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904763 0.0444776 -0.0709897
-0.0752121 0.868494 -0.0306544
0.0414519 -0.0558502 0.720677
Offset = [0.378839, -4.41033, -1.46635]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.908783 0.0463246 -0.0654229
-0.0699135 0.870139 -0.0337351
0.0401221 -0.0519805 0.72027
Offset = [0.0990706, -4.32269, -1.59958]
Background level guess :
first place: 0 (99.9754%)
second place: 87 (0.000697545%)
Guessed background level: 0
[AtlasCreator 02:10:50] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:10:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:10:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case20.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case20.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case20.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
274 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,64.5469,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x119ca50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 -2.17096e-18
1.38778e-17 0.987688 0.156434
-1.92593e-34 -0.156434 0.987688
Offset: [-1.21634, -1.74509, 9.88976]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.21634, 0.836896, 8.54828]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.37069e-17 0.987688 -0.156434
-2.17096e-18 0.156434 0.987688
Singular: 0
Versor: [ -0.0784591, -5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99971 -0.0159332 -0.018051
0.0178853 0.993352 0.11372
0.0161191 -0.114009 0.993349
Offset = [-0.827642, -1.31545, 9.4822]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.953681 0.00905108 -0.0141003
-0.00771349 0.896701 0.0921873
0.0148742 -0.0920656 0.736957
Offset = [-1.32971, -0.195486, 14.2317]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.95789 0.0131842 -0.0228327
0.0365617 0.902543 0.0562865
0.021453 -0.096186 0.730698
Offset = [-1.19865, 0.524235, 14.5659]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.959708 0.00856545 -0.0235465
0.0307702 0.898679 0.0588908
0.0133296 -0.102259 0.732004
Offset = [-1.19104, 0.544694, 14.3911]
Guessed background level: 0
[AtlasCreator 02:14:58] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:15:05] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:15:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case23.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case23.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case23.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 181
LowHigh Thresholds: [0,64.5703,181]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xf45a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.23733, -0.410932, -3.86509]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [1.23733, 2.981, -5.74173]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999766 0.0124666 -0.0176795
-0.00864529 0.979403 0.201732
0.0198302 -0.201532 0.979281
Offset = [0.858538, -0.696836, -3.77331]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 51 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.93171 0.0158739 -0.0400472
-0.00911151 0.867227 0.163707
0.0421039 -0.16319 0.704792
Offset = [1.43487, 1.56578, 1.31627]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.941193 0.0156049 -0.0235811
-0.00478648 0.863518 0.103693
0.030486 -0.192811 0.696651
Offset = [1.24278, 1.96138, 1.53685]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.934918 0.0174917 -0.0314728
-0.00557697 0.864553 0.096448
0.0353148 -0.179507 0.698774
Offset = [1.40858, 2.03466, 1.3689]
Background level guess :
first place: 0 (99.606%)
second place: 143 (0.00759549%)
Guessed background level: 0
[AtlasCreator 02:19:12] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:19:18] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:19:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case26.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case26.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case26.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
259 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 171
LowHigh Thresholds: [0,61.1719,171]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1748a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104385 -0.0054706
0.104528 0.993159 0.0520493
4.33681e-19 -0.052336 0.99863
Offset: [-5.37446, -2.93729, -6.08792]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-6.2141, -2.26284, -6.4898]
Inverse:
0.994522 0.104528 4.33681e-19
-0.104385 0.993159 -0.052336
-0.0054706 0.0520493 0.99863
Singular: 0
Versor: [ -0.0261411, -0.00137, 0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996427 -0.0808325 0.0244792
0.0801044 0.996353 0.0293934
-0.0267659 -0.0273274 0.999268
Offset = [-6.48958, -2.02873, -6.01545]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.955595 -0.0823323 0.0141247
0.0818391 0.955313 0.0325207
-0.0167473 -0.031251 0.768615
Offset = [-6.49384, -1.46627, -1.69659]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 62 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.954916 -0.0786774 0.00326449
0.0934042 0.94838 -0.0114708
-0.0343174 -0.0501338 0.763536
Offset = [-6.0823, -0.569822, -1.69633]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.958784 -0.0772707 0.00949924
0.0863787 0.948456 -0.0048016
-0.0402658 -0.0531027 0.76423
Offset = [-6.54115, -0.522191, -1.68496]
Background level guess :
first place: 0 (99.9778%)
second place: 228 (0.00093006%)
Guessed background level: 0
[AtlasCreator 02:23:26] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:23:33] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:23:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
340 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 240
LowHigh Thresholds: [0,89.9062,240]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xccba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
0.987688 -0.156434 2.17096e-18
0.156434 0.987688 -1.37069e-17
1.92593e-34 1.38778e-17 1
Offset: [-0.700107, 3.33567, -10.8621]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.81197, 3.00002, -10.8621]
Inverse:
0.987688 0.156434 1.92593e-34
-0.156434 0.987688 -1.51574e-35
-1.92593e-34 -1.51574e-35 1
Singular: 0
Versor: [ 6.9175e-18, 5.44419e-19, 0.0784591, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 116 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995506 -0.0942859 0.00878157
0.094214 0.995518 0.00827458
-0.00952238 -0.00741005 0.999927
Offset = [-2.03826, 3.5235, -10.5686]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.85865 -0.0676026 -0.00154792
0.067604 0.874811 0.0447964
-0.00148553 -0.0447985 0.697342
Offset = [-2.11307, 3.51883, -5.28104]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.862143 -0.0666991 -0.00757196
0.0619513 0.879236 0.0299024
-0.00750457 -0.0565152 0.697225
Offset = [-1.91843, 3.83306, -5.34267]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.863759 -0.0690737 -0.0080347
0.0588825 0.875033 0.025035
-0.0156119 -0.0552343 0.696847
Offset = [-1.83812, 3.76352, -5.40604]
Guessed background level: 0
[AtlasCreator 02:27:41] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:27:48] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:27:48] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case29.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case29.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case29.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
228 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 172
LowHigh Thresholds: [0,62.9062,172]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2613a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-7.00048, 0.94424, -6.07396]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-6.44232, 4.40412, -7.9506]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 89 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998372 0.0551408 0.0145677
-0.0570046 0.972793 0.224553
-0.00178938 -0.225018 0.974353
Offset = [-6.87479, 0.0952432, -6.01156]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.880983 0.0165164 -0.0329015
-0.0111452 0.853547 0.157209
0.0350868 -0.156735 0.744326
Offset = [-6.52648, 3.24754, -1.81042]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.876589 0.0145846 -0.0307905
-0.0731332 0.862312 0.0708738
0.042014 -0.186225 0.743821
Offset = [-6.6046, 4.09563, -1.80151]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.875349 0.0237306 -0.0314323
-0.0807586 0.855043 0.0733317
0.0473571 -0.183179 0.741929
Offset = [-6.60232, 4.14532, -2.01887]
Background level guess :
first place: 0 (99.6932%)
second place: 135 (0.00364273%)
Guessed background level: 0
[AtlasCreator 02:32:04] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:32:11] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:32:11] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
324 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,69.3359,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1409a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-5.87292, 3.87909, -1.73384]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-5.87292, 1.11904, -0.812782]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998386 -0.0148937 -0.0548076
0.0131807 0.999417 -0.0314843
0.0552445 0.0307111 0.998
Offset = [-4.9029, 1.22747, -0.0845267]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.879902 -0.0199529 -0.0411672
0.0185577 0.938444 -0.0340001
0.0418147 0.0332006 0.717626
Offset = [-5.49912, 1.51548, 5.0478]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.882238 -0.0191654 -0.0388534
0.0155283 0.939701 -0.0597906
0.0237072 0.017235 0.720346
Offset = [-5.46598, 1.72956, 4.79028]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878912 -0.017682 -0.0446116
0.0144306 0.937544 -0.0647666
0.0327679 0.0237615 0.714542
Offset = [-5.40569, 1.87119, 4.99412]
Background level guess :
first place: 0 (99.9661%)
second place: 125 (0.00100756%)
Guessed background level: 0
[AtlasCreator 02:36:10] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:36:17] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:36:17] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case32.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case32.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case32.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
253 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 162
LowHigh Thresholds: [0,58.4531,162]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1cd8a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [-2.19216, -2.39744, -9.10123]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-2.19216, 0.994487, -10.9779]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999805 -0.0154011 -0.0123783
0.0175958 0.978987 0.203163
0.00898921 -0.203341 0.979067
Offset = [-1.83885, -2.04467, -9.11666]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877532 -0.0435668 -0.0702045
0.0559696 0.895592 0.185728
0.0607795 -0.189022 0.71885
Offset = [-1.37348, -0.597099, -4.18071]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 90 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.871989 -0.0458832 -0.0725296
0.0563263 0.904932 0.0932509
0.0519949 -0.211277 0.709592
Offset = [-1.07934, -0.0350584, -3.93055]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.876406 -0.0374697 -0.0708725
0.0499953 0.89871 0.0982748
0.0490709 -0.213107 0.71427
Offset = [-1.19295, 0.00378688, -4.15512]
Guessed background level: 0
[AtlasCreator 02:40:39] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:40:46] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:40:46] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
224 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 144
LowHigh Thresholds: [0,52.8125,144]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1aa2a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 0.0163519
-0.104528 0.982278 0.155578
1.73472e-18 -0.156434 0.987688
Offset: [4.2262, -4.24075, -12.9044]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [5.26063, -1.54773, -14.2459]
Inverse:
0.994522 -0.104528 1.73472e-18
0.103242 0.982278 -0.156434
0.0163519 0.155578 0.987688
Singular: 0
Versor: [ -0.0783516, 0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997331 0.066915 -0.0292162
-0.0620079 0.987491 0.144973
0.0385517 -0.142775 0.989004
Offset = [5.30302, -3.41514, -11.7075]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904345 0.0473313 -0.0281527
-0.0432096 0.85392 0.132357
0.0341431 -0.13094 0.734474
Offset = [4.86737, -2.09844, -7.53241]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.904127 0.0527959 -0.0447007
-0.0593421 0.864592 0.0512105
0.0297946 -0.166015 0.750715
Offset = [5.42935, -1.44441, -7.95758]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907497 0.0488016 -0.0431232
-0.060632 0.864828 0.0514637
0.0288388 -0.162349 0.743541
Offset = [5.34423, -1.46679, -8.04502]
Background level guess :
first place: 0 (99.8568%)
second place: 144 (0.00224764%)
Guessed background level: 0
[AtlasCreator 02:44:52] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:44:59] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:44:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case36.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case36.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case36.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
273 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,63,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x19bea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4090
Debug: Off
Observers:
none
Matrix:
0.978148 -0.207627 -0.0108813
0.207912 0.976807 0.0511923
8.67362e-19 -0.052336 0.99863
Offset: [-4.28316, -0.0114051, -10.3741]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-5.93596, 0.367175, -10.7759]
Inverse:
0.978148 0.207912 8.67362e-19
-0.207627 0.976807 -0.052336
-0.0108813 0.0511923 0.99863
Singular: 0
Versor: [ -0.0260335, -0.00273624, 0.104493, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 73 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.986363 -0.154848 0.0557659
0.149513 0.984683 0.0896951
-0.0688008 -0.0801342 0.994407
Offset = [-5.61298, -0.823256, -10.0143]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878394 -0.14364 0.0491175
0.137538 0.930734 0.110732
-0.0642513 -0.102694 0.732263
Offset = [-6.20053, -0.950863, -4.76868]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878685 -0.149572 0.0439164
0.114821 0.938513 0.0534989
-0.0785234 -0.111428 0.733026
Offset = [-6.00963, -0.357336, -4.8048]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.882358 -0.151827 0.0425591
0.116141 0.929328 0.0541974
-0.0771897 -0.108827 0.730875
Offset = [-6.14913, -0.455471, -4.56984]
Background level guess :
first place: 0 (99.9645%)
second place: 127 (0.000697545%)
Guessed background level: 0
[AtlasCreator 02:49:10] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:49:17] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:49:17] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case40.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case40.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case40.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 204
LowHigh Thresholds: [0,73.7344,204]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1f7ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 0.104385 0.0054706
-0.104528 0.993159 0.0520493
-8.67362e-19 -0.052336 0.99863
Offset: [2.01322, -1.71738, -13.6795]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [2.87014, -0.713353, -14.0814]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.104385 0.993159 -0.052336
0.0054706 0.0520493 0.99863
Singular: 0
Versor: [ -0.0261411, 0.00137, -0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 62 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997587 0.0693165 0.00402836
-0.0693632 0.992286 0.102744
0.00312461 -0.102776 0.9947
Offset = [2.44586, -2.22223, -13.1067]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.881823 0.0115314 -0.0446304
-0.00743807 0.879931 0.0908183
0.045492 -0.0903898 0.740666
Offset = [2.89433, -0.629651, -7.57682]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.884712 0.0160915 -0.0578998
0.00749351 0.885519 0.0239408
0.0388572 -0.116093 0.7348
Offset = [3.18174, -0.172899, -7.51499]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.880777 0.0225812 -0.0470722
0.00155944 0.881739 0.0197474
0.0338206 -0.109416 0.730785
Offset = [2.98729, 0.0438082, -7.6172]
Background level guess :
first place: 0 (99.8872%)
second place: 69 (0.00271267%)
Guessed background level: 0
[AtlasCreator 02:53:41] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:53:48] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:53:48] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case41.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case41.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case41.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 139
LowHigh Thresholds: [0,50.0625,139]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1be6a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 -2.17096e-18
1.38778e-17 0.987688 0.156434
-1.92593e-34 -0.156434 0.987688
Offset: [-3.20586, -1.49451, -9.85244]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-3.20586, 1.08747, -11.1939]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.37069e-17 0.987688 -0.156434
-2.17096e-18 0.156434 0.987688
Singular: 0
Versor: [ -0.0784591, -5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 44 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999959 0.00885246 -0.00167603
-0.00863506 0.994736 0.102111
0.00257114 -0.102092 0.994772
Offset = [-3.21014, -0.269102, -10.7948]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.890264 -0.00380209 0.0254161
0.00127474 0.909652 0.0987246
-0.0256673 -0.0986596 0.738302
Offset = [-3.98917, 0.507857, -5.30204]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.890843 0.00457432 0.0172336
-0.0139647 0.908449 0.0401795
-0.0537443 -0.119867 0.727525
Offset = [-3.95772, 1.22041, -5.36172]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.88879 0.00155026 0.0167054
-0.0173142 0.90767 0.0378237
-0.0482161 -0.113879 0.725863
Offset = [-3.86218, 1.2267, -5.3087]
Guessed background level: 0
[AtlasCreator 02:57:57] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 02:58:04] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 02:58:04] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case42.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case42.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case42.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 190
LowHigh Thresholds: [0,70.1172,190]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2169a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [-0.48053, -1.66868, -18.0957]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [0.0352328, 0.982361, -19.4372]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 68 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999834 -0.0181539 -0.00137735
0.0181703 0.990265 0.138002
-0.00114134 -0.138005 0.990431
Offset = [0.0700772, -0.885788, -17.8804]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.88359 0.00463345 -0.0192353
-0.00140074 0.8925 0.164782
0.0197359 -0.164723 0.718802
Offset = [-0.259622, -0.338475, -13.0837]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.879272 -0.00281057 -0.0339309
-0.0165635 0.892588 0.0940665
0.00973008 -0.185412 0.70903
Offset = [0.136498, 0.484524, -12.9918]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.879007 0.00413216 -0.0276878
-0.0189626 0.891268 0.0982137
0.00422074 -0.185598 0.709457
Offset = [0.0691006, 0.354018, -13.0093]
Background level guess :
first place: 0 (99.7911%)
second place: 120 (0.00356523%)
Guessed background level: 0
[AtlasCreator 03:02:16] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:02:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:02:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case46.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case46.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case46.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
226 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,54.4219,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2666a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [4.81451, 3.40156, -1.39185]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [4.63226, -0.393764, -0.261436]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 71 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999624 -0.0274322 0.000219053
0.0269842 0.981796 -0.188013
0.00494254 0.187948 0.982167
Offset = [4.31623, 2.75033, -0.867645]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898368 -0.0167689 0.0203952
0.0195602 0.912921 -0.145423
-0.0177358 0.145772 0.752424
Offset = [4.05961, 3.12521, 2.9738]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.899968 -0.0115232 0.0100983
-0.0191315 0.908331 -0.152062
-0.0505275 0.141999 0.758801
Offset = [4.31795, 3.15572, 2.88455]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898551 -0.013722 0.00536103
-0.0184098 0.905174 -0.156027
-0.0464007 0.138208 0.754241
Offset = [4.48541, 3.48619, 2.7412]
Guessed background level: 0
[AtlasCreator 03:06:26] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:06:34] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:06:34] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case47.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case47.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case47.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
287 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 173
LowHigh Thresholds: [0,63.25,173]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xd3da50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [-5.76037, -0.874578, 0.449894]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-5.99223, -3.72326, 1.37095]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 51 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999724 -0.00900679 -0.0217057
0.00649614 0.993565 -0.11308
0.0225845 0.112908 0.993349
Offset = [-6.17389, -1.99671, 1.0997]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 105 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.90013 -0.00757505 0.0157725
0.00829235 0.851608 -0.0459201
-0.0154075 0.0460439 0.735583
Offset = [-6.69266, -1.72261, 6.08511]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902204 -0.000582079 0.00535561
0.0328306 0.844268 -0.0664121
-0.018635 0.0507476 0.741636
Offset = [-6.43216, -1.49125, 6.10911]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.90114 -0.00297872 0.00471128
0.0346873 0.849202 -0.0580455
-0.02147 0.0409272 0.737685
Offset = [-6.41579, -1.544, 6.11294]
Guessed background level: 0
[AtlasCreator 03:10:47] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:10:55] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:10:55] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case48.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case48.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case48.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
205 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 133
LowHigh Thresholds: [0,47.8047,133]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xb38a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.994522 0.103956 -0.0109262
-0.104528 0.989074 -0.103956
-8.67362e-19 0.104528 0.994522
Offset: [0.51709, 1.09223, -11.0459]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [1.09093, -0.596971, -10.3836]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.103956 0.989074 0.104528
-0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, -0.00273905, -0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995615 0.0904671 -0.023798
-0.0921206 0.992422 -0.0813116
0.0162617 0.0831473 0.996405
Offset = [0.174475, -0.620444, -9.75557]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 85 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.924612 0.0792255 -0.0299901
-0.0797762 0.884644 -0.0176316
0.0284929 0.0199607 0.73786
Offset = [0.584746, -0.600145, -4.30655]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.919941 0.0756668 -0.0475923
-0.0389498 0.87411 -0.0755779
0.0353397 -0.0186315 0.727461
Offset = [0.8466, 0.969888, -4.37938]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.918594 0.0643066 -0.0495709
-0.0267176 0.881631 -0.0786475
0.0384498 -0.0207351 0.729216
Offset = [0.703947, 0.990346, -4.54762]
Background level guess :
first place: 0 (99.7032%)
second place: 148 (0.00596788%)
Guessed background level: 0
[AtlasCreator 03:15:16] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:15:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:15:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 176
LowHigh Thresholds: [0,63.2109,176]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2985a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0516916 0.00818715
-0.052336 0.986335 0.15622
0 -0.156434 0.987688
Offset: [1.24577, 2.16634, -16.7068]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [1.76153, 4.81739, -18.0482]
Inverse:
0.99863 -0.052336 0
0.0516916 0.986335 -0.156434
0.00818715 0.15622 0.987688
Singular: 0
Versor: [ -0.0784322, 0.00205382, -0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998497 0.0452068 0.0309837
-0.0484147 0.992516 0.112109
-0.0256837 -0.11344 0.993213
Offset = [1.0215, 2.53124, -17.1359]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.927935 0.0330086 0.0234766
-0.0358437 0.94511 0.132892
-0.0188666 -0.133625 0.795339
Offset = [0.523445, 3.23058, -12.5461]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.929364 0.0292735 0.0115655
-0.051131 0.933395 0.0928662
-0.0325307 -0.16277 0.779484
Offset = [0.903103, 3.7105, -12.2887]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.931566 0.0387703 0.0193936
-0.0576345 0.945256 0.086406
-0.0429829 -0.162523 0.775809
Offset = [0.917382, 3.71055, -12.4871]
Background level guess :
first place: 0 (99.5194%)
second place: 159 (0.00658792%)
Guessed background level: 0
[AtlasCreator 03:19:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:19:37] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:19:37] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case51.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case51.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case51.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
265 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 174
LowHigh Thresholds: [0,63.7031,174]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xde4a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 -0.0108813
-0.052336 0.976807 -0.207627
8.67362e-19 0.207912 0.978148
Offset: [1.7696, 0.581147, 7.30059]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [1.95617, -3.04916, 8.431]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0511923 0.976807 0.207912
-0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998834 0.0354285 0.032806
-0.029853 0.987129 -0.157115
-0.0379501 0.155952 0.987035
Offset = [1.54661, -0.66032, 7.9409]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878542 0.0258081 0.0220481
-0.0226418 0.930218 -0.133429
-0.0252888 0.132853 0.751818
Offset = [0.862928, -0.720386, 12.6378]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.882356 0.022393 0.0247215
-0.0248273 0.932313 -0.143803
-0.0377805 0.119563 0.753326
Offset = [0.94421, -0.368555, 12.6097]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.879225 0.0258341 0.0201353
-0.0298545 0.923491 -0.150816
-0.0362421 0.128048 0.753816
Offset = [1.10305, -0.172371, 12.689]
Background level guess :
first place: 0 (99.921%)
second place: 111 (0.00124008%)
Guessed background level: 0
[AtlasCreator 03:23:28] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:23:35] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:23:35] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case53.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case53.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case53.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
309 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 195
LowHigh Thresholds: [0,72.1875,195]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1d0ba50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 0.0520493 -0.0054706
-0.052336 0.993159 -0.104385
4.33681e-19 0.104528 0.994522
Offset: [1.48173, 2.19752, -6.8764]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [1.76689, 0.448247, -6.21403]
Inverse:
0.99863 -0.052336 4.33681e-19
0.0520493 0.993159 0.104528
-0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999298 0.0348704 0.0137181
-0.0342582 0.998506 -0.0425802
-0.0151824 0.0420803 0.998999
Offset = [1.0429, 0.933314, -6.64477]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 64 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.921939 0.0337726 -0.00681865
-0.0339471 0.922194 -0.0273584
0.00588821 0.0275736 0.766601
Offset = [1.23123, 1.90778, -1.34664]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.923854 0.0333054 -0.0107439
-0.0337938 0.910794 -0.0655796
-0.0185443 0.0174677 0.759626
Offset = [1.26493, 2.51062, -1.31569]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.922221 0.0389439 -0.0145323
-0.0391929 0.914584 -0.0568055
-0.014395 0.00594046 0.762654
Offset = [1.33345, 2.56754, -1.57341]
Guessed background level: 0
[AtlasCreator 03:27:54] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:28:02] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:28:02] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case54.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case54.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case54.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
295 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 196
LowHigh Thresholds: [0,73.4062,196]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e58a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-3.46404, 1.47238, -2.13072]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-2.90588, 4.93226, -4.00736]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999503 0.00203033 0.0314642
-0.00795127 0.981902 0.189222
-0.0305105 -0.189379 0.98143
Offset = [-3.82175, 1.75235, -2.29467]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.868555 0.00826244 0.00614612
-0.00886108 0.827236 0.104776
-0.00524634 -0.104825 0.705569
Offset = [-3.75259, 5.18116, 2.16306]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.867553 0.0140995 0.00101688
-0.0273857 0.828852 0.038983
-0.016871 -0.132624 0.695922
Offset = [-3.5749, 5.95344, 2.51045]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.87533 0.0145492 0.000584417
-0.0267935 0.826225 0.036172
-0.016148 -0.127757 0.69437
Offset = [-3.69338, 5.81036, 2.55414]
Background level guess :
first place: 0 (99.8487%)
second place: 86 (0.00263517%)
Guessed background level: 0
[AtlasCreator 03:31:59] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:32:06] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:32:06] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case57.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case57.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case57.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
264 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 169
LowHigh Thresholds: [0,60.8125,169]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xadda50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4090
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-1.64739, 2.88686, -0.149139]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.82964, -0.90846, 0.981275]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99981 -0.0125704 0.0148708
0.0144916 0.990455 -0.137075
-0.0130058 0.137265 0.990449
Offset = [-2.34741, 1.1455, 0.398547]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 69 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.901247 -0.00806171 0.0135017
0.00894371 0.901192 -0.0665926
-0.0129343 0.0667051 0.731358
Offset = [-2.3754, 1.14161, 5.33176]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911881 -0.0163468 0.0117587
0.0217587 0.898921 -0.0827478
-0.0237799 0.0447174 0.727885
Offset = [-2.34855, 1.63694, 5.35924]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.907213 -0.00976155 0.0103829
0.0250101 0.89279 -0.0934715
-0.0210705 0.0486143 0.721275
Offset = [-2.23593, 1.76351, 5.4752]
Guessed background level: 0
[AtlasCreator 03:36:16] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:36:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:36:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case59.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case59.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case59.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
277 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,70.0312,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1868a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 -0.0163519
-0.104528 0.982278 -0.155578
0 0.156434 0.987688
Offset: [1.60436, 1.76576, -4.05903]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [2.0804, -0.85399, -3.13797]
Inverse:
0.994522 -0.104528 0
0.103242 0.982278 0.156434
-0.0163519 -0.155578 0.987688
Singular: 0
Versor: [ 0.0783516, -0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997254 0.056229 0.0481896
-0.0499882 0.991252 -0.122146
-0.0546362 0.119402 0.991342
Offset = [0.595217, 1.00357, -4.09511]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.895883 0.0605156 0.0193415
-0.0596942 0.870684 -0.0405456
-0.0217447 0.0393091 0.74204
Offset = [1.12397, 0.229357, 2.30924]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.897583 0.0646012 0.00575414
-0.0418471 0.868594 -0.0664652
-0.0317633 0.0154747 0.73843
Offset = [1.25648, 0.620541, 2.28677]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902429 0.0618492 -0.000591626
-0.0382888 0.870462 -0.063129
-0.0350218 0.0196381 0.738348
Offset = [1.34842, 0.794342, 2.25064]
Guessed background level: 0
[AtlasCreator 03:40:26] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:40:34] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:40:34] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case60.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case60.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case60.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
338 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 239
LowHigh Thresholds: [0,90.25,239]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1210a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.987688 0.154508 -0.0244717
-0.156434 0.975528 -0.154508
-3.46945e-18 0.156434 0.987688
Offset: [-2.38453, 3.51508, -2.05853]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.66562, 0.946604, -1.13748]
Inverse:
0.987688 -0.156434 -3.46945e-18
0.154508 0.975528 0.156434
-0.0244717 -0.154508 0.987688
Singular: 0
Versor: [ 0.0782172, -0.00615583, -0.0782172, 0.993844 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 88 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.990109 0.140214 -0.00489203
-0.139996 0.985083 -0.100066
-0.00921158 0.0997612 0.994969
Offset = [-2.48283, 1.51151, -1.70047]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 59 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.87353 0.0331148 -0.0541207
-0.0299177 0.87801 0.0588509
0.0559515 -0.0571131 0.69731
Offset = [-1.6035, 1.22733, 5.36671]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.867899 0.0344577 -0.0597762
-0.0343796 0.873974 0.00152351
0.0519934 -0.0812447 0.682835
Offset = [-1.59656, 1.98216, 5.54727]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.867144 0.0321607 -0.0597646
-0.0283886 0.87357 0.00369515
0.0482156 -0.0786251 0.680816
Offset = [-1.50321, 2.00809, 5.51898]
Background level guess :
first place: 0 (99.929%)
second place: 112 (0.00186012%)
Guessed background level: 0
[AtlasCreator 03:44:50] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:44:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:44:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case61.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case61.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case61.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
237 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 150
LowHigh Thresholds: [0,53.9062,150]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1e53a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-1.28732, -0.733295, 4.58433]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.46957, -4.52861, 5.71475]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996108 -0.0274751 0.0837531
0.050212 0.95781 -0.282983
-0.0724446 0.286087 0.955461
Offset = [-3.08624, 0.810075, 4.43337]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.933828 -0.0257603 0.0533634
0.0366149 0.875614 -0.213684
-0.0465897 0.215262 0.725702
Offset = [-2.52323, -0.299185, 9.47534]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.933177 -0.021614 0.0419138
0.0512939 0.867836 -0.230967
-0.0654896 0.211071 0.731502
Offset = [-2.26812, 0.297954, 9.13745]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.932044 -0.0234415 0.0422163
0.0590208 0.879137 -0.22766
-0.0662588 0.207551 0.72878
Offset = [-2.14243, 0.237416, 9.21107]
Background level guess :
first place: 0 (99.9685%)
second place: 147 (0.000852555%)
Guessed background level: 0
[AtlasCreator 03:48:53] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:49:01] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:49:01] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case62.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case62.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case62.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
252 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 170
LowHigh Thresholds: [0,62.1562,170]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1861a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-3.47777, 7.18346, -1.1802]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-3.47777, 4.42341, -0.259144]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 390 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99971 -0.00882441 -0.0224048
0.00780102 0.99894 -0.0453606
0.0227814 0.0451726 0.998719
Offset = [-3.64331, 3.55421, 0.548954]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911349 -0.0147219 0.000639706
0.014704 0.863263 0.0222511
-0.000967057 -0.0222393 0.712357
Offset = [-3.89488, 4.03555, 6.30458]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.905455 -0.0223078 -0.0118621
0.0164989 0.860411 -0.039599
-0.0145143 -0.0421238 0.717203
Offset = [-3.54385, 5.75568, 5.80157]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.906632 -0.0199897 -0.0141902
0.0109102 0.863156 -0.0426252
-0.0156039 -0.0451669 0.717105
Offset = [-3.32205, 5.61763, 5.79852]
Background level guess :
first place: 0 (99.5161%)
second place: 137 (0.00713046%)
Guessed background level: 0
[AtlasCreator 03:54:20] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:54:28] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:54:28] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/case8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
263 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 160
LowHigh Thresholds: [0,58.2422,160]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2a6fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [0.505495, -1.07525, 7.47729]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [0.224664, -2.98954, 8.13966]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999985 -0.00266354 -0.0047139
0.00217656 0.994939 -0.100455
0.00495761 0.100443 0.99493
Offset = [0.672533, -0.709839, 9.30287]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 87 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.822483 -0.0301625 -0.0271612
0.0290303 0.952486 -0.0411562
0.0283681 0.0403338 0.732608
Offset = [0.167696, -1.18522, 12.7793]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.825578 -0.0323445 -0.0303112
0.019274 0.944966 -0.0709284
0.00917834 0.0275221 0.727004
Offset = [0.390057, -0.701431, 12.6489]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.829827 -0.0273693 -0.0232429
0.0191265 0.946044 -0.0639998
0.00426039 0.0173092 0.723088
Offset = [0.0100671, -0.668787, 12.9494]
Background level guess :
first place: 0 (99.7564%)
second place: 38 (0.00302269%)
Guessed background level: 0
[AtlasCreator 03:58:39] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 03:58:47] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 03:58:47] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG1.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG1.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG1.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
347 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 234
LowHigh Thresholds: [0,86.4844,234]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xb40a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.994522 0.104385 -0.0054706
-0.104528 0.993159 -0.0520493
4.33681e-19 0.052336 0.99863
Offset: [0.866872, -1.79637, 5.13966]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [1.53697, -2.56976, 5.49473]
Inverse:
0.994522 -0.104528 4.33681e-19
0.104385 0.993159 0.052336
-0.0054706 -0.0520493 0.99863
Singular: 0
Versor: [ 0.0261411, -0.00137, -0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 68 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995688 0.0614244 -0.0695163
-0.0611039 0.998109 0.00672839
0.0697981 -0.00245166 0.997558
Offset = [2.12224, -2.32123, 5.59573]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.884256 0.0434012 -0.0777045
-0.0430097 0.930161 0.00670556
0.0779219 -0.00333691 0.765189
Offset = [2.22861, -1.47718, 10.2249]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 8 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.887149 0.0503349 -0.0788515
-0.021624 0.928857 0.000486103
0.0690516 -0.00498103 0.766858
Offset = [2.09596, -1.25997, 10.1374]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.886179 0.0497547 -0.0769989
-0.0266896 0.931464 -0.00276124
0.0728532 -0.00068227 0.767842
Offset = [2.03919, -1.35811, 10.0796]
Background level guess :
first place: 0 (99.7627%)
second place: 186 (0.00410776%)
Guessed background level: 0
[AtlasCreator 04:02:54] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:03:02] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:03:02] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 215
LowHigh Thresholds: [0,80.8828,215]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x228da50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0516916 0.00818715
0.052336 0.986335 -0.15622
0 0.156434 0.987688
Offset: [3.53655, 3.56603, 16.0892]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [3.30469, 0.717342, 17.0103]
Inverse:
0.99863 0.052336 0
-0.0516916 0.986335 0.156434
0.00818715 -0.15622 0.987688
Singular: 0
Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 75 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997774 -0.0655449 -0.0122684
0.0633295 0.98903 -0.133452
0.0208809 0.132378 0.990979
Offset = [3.8799, 3.5944, 16.602]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877663 -0.0572751 -0.024764
0.0555409 0.920525 -0.0658095
0.0284412 0.0643058 0.743272
Offset = [3.46947, 2.71, 22.3284]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.87856 -0.0537294 -0.0248303
0.0410197 0.91278 -0.118921
0.00360131 0.0349043 0.729584
Offset = [3.66882, 3.26037, 22.2522]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.879259 -0.0553389 -0.0243756
0.0449008 0.91316 -0.120337
0.00349179 0.0431366 0.732327
Offset = [3.60161, 3.46934, 22.1819]
Background level guess :
first place: 0 (99.8225%)
second place: 6 (0.00767299%)
Guessed background level: 0
[AtlasCreator 04:07:06] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:07:14] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:07:14] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG11.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG11.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG11.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.7344,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1aa9a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4054
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [3.47683, 0.337934, 9.05942]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [3.47683, -2.42211, 9.98048]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99982 0.0121577 0.0145427
-0.010391 0.993203 -0.11593
-0.0158533 0.115758 0.993151
Offset = [3.61393, -0.393723, 9.51967]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.872299 0.0136042 0.0232057
-0.0126374 0.893949 -0.0413132
-0.0237461 0.041005 0.737209
Offset = [2.42724, -0.505367, 14.7759]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.870017 0.0133702 0.0139404
-0.00524021 0.897377 -0.0671383
-0.0508028 0.0256395 0.730613
Offset = [2.67189, -0.217208, 14.7845]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.871414 0.0147938 0.0109422
-0.015033 0.899083 -0.0696075
-0.0506043 0.0322409 0.735019
Offset = [2.85031, -0.45269, 14.7001]
Guessed background level: 0
[AtlasCreator 04:11:12] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:11:20] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:11:20] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
321 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 226
LowHigh Thresholds: [0,85.5,226]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1f21a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
1 -1.37069e-17 2.17096e-18
1.38778e-17 0.987688 -0.156434
1.92593e-34 0.156434 0.987688
Offset: [-1.36329, 2.31035, 0.625807]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.36329, -0.4497, 1.54686]
Inverse:
1 1.38778e-17 1.92593e-34
-1.37069e-17 0.987688 0.156434
2.17096e-18 -0.156434 0.987688
Singular: 0
Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999707 -0.0216464 0.0108761
0.0228808 0.991197 -0.130403
-0.00795758 0.130613 0.991401
Offset = [-1.14753, 1.8353, 0.6135]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.849659 -0.00716207 0.0223364
0.00733257 0.869073 -0.00756082
-0.0222811 0.00772253 0.708839
Offset = [-2.33551, 0.803277, 7.51427]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.851936 -0.00595592 0.0068379
-0.0140592 0.863073 -0.0621285
-0.0462896 -0.0129172 0.700228
Offset = [-1.7576, 1.60436, 7.40496]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.849843 -0.00676876 0.00851243
-0.00862403 0.862712 -0.0581025
-0.0515728 -0.0119763 0.699009
Offset = [-1.88629, 1.62519, 7.57249]
Background level guess :
first place: 0 (99.7555%)
second place: 81 (0.00325521%)
Guessed background level: 0
[AtlasCreator 04:15:19] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:15:27] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:15:27] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG13.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG13.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG13.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
336 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 229
LowHigh Thresholds: [0,85.0938,229]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xe15a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4063
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [-0.998784, 0.91056, 11.7808]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.27962, -1.00373, 12.4432]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997431 -0.0208671 0.0685343
0.0253501 0.99755 -0.0652084
-0.0670057 0.0667782 0.995515
Offset = [-2.44172, 0.1912, 12.4319]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.912269 -0.0204787 0.0425098
0.0219667 0.918934 -0.0348392
-0.0417603 0.0357342 0.75004
Offset = [-2.1255, -0.0579948, 17.3871]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.912694 -0.0228265 0.0288072
0.0470395 0.919763 -0.063411
-0.0520662 0.0166418 0.748372
Offset = [-1.81961, 0.538012, 17.1564]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.916287 -0.0150858 0.034733
0.0340693 0.921704 -0.0655829
-0.0558459 0.020801 0.745807
Offset = [-2.0156, 0.511739, 17.2498]
Background level guess :
first place: 0 (98.828%)
second place: 187 (0.0134859%)
Guessed background level: 0
[AtlasCreator 04:19:36] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:19:44] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:19:44] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
348 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,80.2812,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x14dea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.16537, 3.1649, 13.0607]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [3.16537, -0.543082, 14.1911]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99979 -0.00699111 0.0192623
0.0110174 0.97597 -0.217628
-0.0172779 0.217795 0.975842
Offset = [2.54527, 3.13447, 13.3439]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.917844 0.000475007 0.00860485
0.00110935 0.946209 -0.183185
-0.00854626 0.183187 0.789336
Offset = [2.39807, 2.154, 17.8777]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.918918 0.000468874 0.00328776
0.0114021 0.938029 -0.188867
-0.0407362 0.186066 0.790931
Offset = [2.58704, 2.39263, 17.7179]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.929005 -0.00255512 -0.00137981
0.0164683 0.939421 -0.187755
-0.0404182 0.186043 0.791167
Offset = [2.80379, 2.56671, 17.6957]
Background level guess :
first place: 0 (99.838%)
second place: 81 (0.00387525%)
Guessed background level: 0
[AtlasCreator 04:23:46] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:23:54] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:23:54] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
271 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 186
LowHigh Thresholds: [0,69.8438,186]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x26d2a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4078
Debug: Off
Observers:
none
Matrix:
0.994522 -0.103242 -0.0163519
0.104528 0.982278 0.155578
-3.46945e-18 -0.156434 0.987688
Offset: [1.2056, -3.93557, -2.57852]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [0.188439, -1.57213, -3.92]
Inverse:
0.994522 0.104528 -3.46945e-18
-0.103242 0.982278 -0.156434
-0.0163519 0.155578 0.987688
Singular: 0
Versor: [ -0.0783516, -0.00410623, 0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.997676 -0.0628535 -0.0263056
0.0656242 0.990258 0.122807
0.0183305 -0.124248 0.992082
Offset = [0.880635, -3.15964, -2.93835]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 43 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.902159 -0.0488735 -0.0229858
0.0511128 0.910012 0.109838
0.0174483 -0.110853 0.763899
Offset = [0.643158, -2.20525, 2.40637]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911824 -0.0425026 -0.0264153
0.104942 0.912468 0.0358698
0.00824986 -0.146291 0.768085
Offset = [0.649401, -1.19648, 2.12302]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.911471 -0.0409003 -0.0232164
0.105922 0.906942 0.0374003
-0.000469275 -0.145586 0.772726
Offset = [0.681101, -1.13192, 1.88126]
Guessed background level: 0
[AtlasCreator 04:27:57] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:28:05] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:28:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG16.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG16.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG16.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 225
LowHigh Thresholds: [0,84.6094,225]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x189fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [-1.75244, 3.25005, -4.87124]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.93469, -0.545266, -3.74082]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 99 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998934 -0.0392002 -0.0243749
0.0345669 0.985212 -0.167815
0.0305928 0.166793 0.985517
Offset = [-1.32246, 1.95468, -4.49549]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.851434 -0.0269047 -0.0355657
0.0258734 0.843292 -0.0291442
0.0363228 0.028195 0.68881
Offset = [-1.89363, 0.868625, 2.86792]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.851743 -0.0198972 -0.0446125
0.0471175 0.841743 -0.0829346
0.0217148 0.0156291 0.688369
Offset = [-1.64702, 1.68085, 2.46069]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.856144 -0.0171745 -0.0399695
0.0433645 0.843488 -0.0875852
0.0143635 0.0100691 0.690931
Offset = [-1.60786, 1.7479, 2.11257]
Background level guess :
first place: 0 (99.6543%)
second place: 214 (0.00496032%)
Guessed background level: 0
[AtlasCreator 04:32:22] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:32:31] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:32:31] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG17.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG17.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG17.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
373 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 246
LowHigh Thresholds: [0,90.8516,246]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x23c5a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4087
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 -0.0108813
-0.052336 0.976807 -0.207627
8.67362e-19 0.207912 0.978148
Offset: [4.90554, 3.56985, 13.6774]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [5.09211, -0.0604555, 14.8079]
Inverse:
0.99863 -0.052336 8.67362e-19
0.0511923 0.976807 0.207912
-0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999114 0.0420759 -0.000128717
-0.0417135 0.990099 -0.134031
-0.00551203 0.133918 0.990977
Offset = [4.70773, 2.31898, 14.0021]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.900791 0.0462354 0.00985508
-0.0447011 0.925842 -0.12136
-0.0153834 0.120784 0.746643
Offset = [4.08582, 3.23473, 19.0797]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898259 0.0451304 -0.00881682
-0.0371187 0.915145 -0.161036
-0.0475169 0.107103 0.746891
Offset = [4.4935, 3.86478, 18.7814]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.89579 0.0457847 -0.00857588
-0.0359658 0.917998 -0.161674
-0.0370271 0.106919 0.735312
Offset = [4.24615, 3.9922, 19.2428]
Guessed background level: 0
[AtlasCreator 04:36:28] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:36:36] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:36:36] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
280 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 201
LowHigh Thresholds: [0,73.75,201]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xe19a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
0.994522 0.103242 0.0163519
-0.104528 0.982278 0.155578
1.73472e-18 -0.156434 0.987688
Offset: [3.82894, -2.87374, -1.7476]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [4.86337, -0.18073, -3.08908]
Inverse:
0.994522 -0.104528 1.73472e-18
0.103242 0.982278 -0.156434
0.0163519 0.155578 0.987688
Singular: 0
Versor: [ -0.0783516, 0.00410623, -0.0521746, 0.995551 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.994277 0.090227 -0.057198
-0.0813008 0.986413 0.142758
0.0693015 -0.137291 0.988103
Offset = [4.90791, -3.23809, -1.67641]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.916245 0.0748774 -0.0583624
-0.0675112 0.868496 0.119324
0.0667459 -0.114845 0.761849
Offset = [4.71771, -1.2878, 3.27819]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.927789 0.0799319 -0.0686349
-0.012112 0.871311 0.0697804
0.0515914 -0.134295 0.755865
Offset = [4.95878, -0.651035, 3.24814]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928297 0.0876943 -0.06569
-0.0138587 0.870516 0.0713532
0.0536189 -0.137134 0.756733
Offset = [4.97407, -0.669429, 3.23128]
Guessed background level: 0
[AtlasCreator 04:40:43] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:40:52] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:40:52] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
266 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,66.2812,177]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1d74a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4066
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [1.77811, -3.00916, -0.337678]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [1.77811, 0.382764, -2.21432]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999974 0.00194836 -0.00696214
-0.000507256 0.979536 0.201266
0.00721181 -0.201258 0.979512
Offset = [1.41366, -2.9716, -0.361313]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 136 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.920736 -0.000919143 -0.00856835
0.00214893 0.883843 0.144646
0.00834526 -0.144659 0.75205
Offset = [1.69527, -0.778108, 4.07593]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.926711 -0.00481696 -0.0155908
0.000615878 0.883143 0.0737397
-0.00197746 -0.177564 0.735576
Offset = [1.83138, -0.083658, 4.23177]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.928796 -0.0091686 -0.0127124
0.00317317 0.879181 0.072156
-0.00862276 -0.179237 0.733658
Offset = [1.81814, -0.010584, 3.9938]
Background level guess :
first place: 0 (99.81%)
second place: 65 (0.00279018%)
Guessed background level: 0
[AtlasCreator 04:45:29] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:45:37] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:45:37] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
294 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,69.1875,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x28c2a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0520493 0.0054706
0.052336 0.993159 -0.104385
-8.67362e-19 0.104528 0.994522
Offset: [4.10366, 3.23101, 15.1937]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [3.82283, 1.31672, 15.856]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0520493 0.993159 0.104528
0.0054706 -0.104385 0.994522
Singular: 0
Versor: [ 0.052318, 0.00137, 0.0261411, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998993 -0.0382781 -0.0233945
0.0369684 0.997853 -0.0540636
0.0254137 0.0531443 0.998263
Offset = [4.32849, 1.18383, 16.0484]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 60 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.889507 -0.0283129 -0.0130828
0.0278162 0.911846 -0.0366994
0.014108 0.0363176 0.74529
Offset = [4.13388, 2.232, 20.1288]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.880655 -0.0291378 -0.0234247
0.0674219 0.903216 -0.0491781
-7.1128e-05 0.0197196 0.739149
Offset = [4.35063, 2.97646, 20.1338]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.885384 -0.0270713 -0.01856
0.0609949 0.90309 -0.0502617
-0.00534232 0.0246557 0.734522
Offset = [4.14786, 3.00491, 20.4747]
Background level guess :
first place: 0 (99.9727%)
second place: 101 (0.0016276%)
Guessed background level: 0
[AtlasCreator 04:49:48] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:49:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:49:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
337 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 227
LowHigh Thresholds: [0,84.7656,227]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x215da50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4081
Debug: Off
Observers:
none
Matrix:
0.978148 -0.207912 2.88535e-18
0.207912 0.978148 -1.35745e-17
1.92593e-34 1.38778e-17 1
Offset: [-1.25141, 3.13181, 9.0316]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-2.72049, 2.64601, 9.0316]
Inverse:
0.978148 0.207912 1.92593e-34
-0.207912 0.978148 1.38778e-17
2.88535e-18 -1.35745e-17 1
Singular: 0
Versor: [ 6.90088e-18, 7.25312e-19, 0.104528, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.98778 -0.155848 0.00113576
0.155822 0.987707 0.0124098
-0.00305583 -0.0120812 0.999922
Offset = [-1.87559, 2.78272, 9.29552]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 35 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.878115 -0.120666 0.0317963
0.119296 0.888271 0.0419489
-0.0366029 -0.0378279 0.785365
Offset = [-3.00611, 3.51935, 13.7917]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.883243 -0.121724 0.0282697
0.0987307 0.881575 -0.0199495
-0.0593931 -0.074824 0.77627
Offset = [-2.91597, 4.16824, 13.8448]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.880812 -0.12296 0.0275732
0.0993526 0.883328 -0.0243473
-0.0565161 -0.0700704 0.785184
Offset = [-2.92381, 4.1181, 13.6402]
Background level guess :
first place: 0 (99.8485%)
second place: 76 (0.00217014%)
Guessed background level: 0
[AtlasCreator 04:53:55] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:54:04] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:54:04] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG4.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG4.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG4.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
299 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 205
LowHigh Thresholds: [0,75.9375,205]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1d2ea50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.994522 0.102244 -0.0217327
-0.104528 0.972789 -0.206773
-1.73472e-18 0.207912 0.978148
Offset: [0.598389, 1.73341, 17.7934]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [0.975342, -1.82909, 18.9238]
Inverse:
0.994522 -0.104528 -1.73472e-18
0.102244 0.972789 0.207912
-0.0217327 -0.206773 0.978148
Singular: 0
Versor: [ 0.104385, -0.0054706, -0.0520493, 0.993159 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.996781 0.0733706 -0.0323042
-0.0779161 0.981478 -0.175013
0.018865 0.176967 0.984036
Offset = [1.3534, 1.48407, 18.0605]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.815672 -0.00106764 -0.0382535
-0.00299796 0.922141 -0.106065
0.0381508 0.106102 0.679336
Offset = [0.655119, 0.752618, 24.7198]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.812861 0.00274909 -0.0301201
0.00624804 0.913479 -0.135666
0.0262317 0.103469 0.675084
Offset = [0.640137, 0.942852, 24.8807]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.812841 0.000836381 -0.0370385
0.00799371 0.915672 -0.12854
0.0321413 0.103637 0.676432
Offset = [0.660221, 0.832665, 24.7618]
Background level guess :
first place: 0 (99.959%)
second place: 76 (0.00139509%)
Guessed background level: 0
[AtlasCreator 04:58:00] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 04:58:09] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 04:58:09] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
332 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 223
LowHigh Thresholds: [0,82.5,223]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x2893a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
1 -1.35745e-17 2.88535e-18
1.38778e-17 0.978148 -0.207912
1.92593e-34 0.207912 0.978148
Offset: [3.44508, 6.04183, 5.15873]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [3.44508, 2.33385, 6.28914]
Inverse:
1 1.38778e-17 1.92593e-34
-1.35745e-17 0.978148 0.207912
2.88535e-18 -0.207912 0.978148
Singular: 0
Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999757 -0.0203896 -0.00837657
0.0183449 0.980298 -0.196672
0.0122216 0.19647 0.980434
Offset = [4.12167, 5.2973, 5.46989]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.897457 -0.023378 0.00132091
0.0233965 0.870368 -0.0963224
0.000937419 0.0963269 0.71347
Offset = [2.91073, 5.44787, 11.1919]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.900868 -0.0221355 -0.0043414
0.0253796 0.866706 -0.132356
-0.00473318 0.0825636 0.71289
Offset = [3.12899, 6.06908, 10.956]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.898524 -0.0242892 -0.00821579
0.0289717 0.870853 -0.131975
-0.00164655 0.0863654 0.710768
Offset = [3.169, 6.04565, 10.9526]
Background level guess :
first place: 0 (99.998%)
second place: 84 (0.00031002%)
Guessed background level: 0
[AtlasCreator 05:02:15] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 05:02:24] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 05:02:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG6.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG6.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG6.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
286 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 209
LowHigh Thresholds: [0,77.25,209]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x186fa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4069
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 -0.0108813
0.052336 0.976807 0.207627
8.67362e-19 -0.207912 0.978148
Offset: [1.05791, 1.55474, 1.37416]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [0.504076, 4.8496, -0.502483]
Inverse:
0.99863 0.052336 8.67362e-19
-0.0511923 0.976807 -0.207912
-0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, -0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999287 -0.0374505 0.00468777
0.035391 0.972922 0.228406
-0.0131148 -0.228078 0.973555
Offset = [-0.0377786, 0.869773, 1.95098]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.828884 -0.0347344 -0.00299525
0.0345132 0.854186 0.225857
-0.00492898 -0.225823 0.734373
Offset = [0.0234403, 2.49608, 6.22804]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.826721 -0.0397716 -0.016807
0.0277042 0.853284 0.169269
-0.0192322 -0.244064 0.732815
Offset = [0.455663, 3.21614, 6.22394]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.828495 -0.0348423 -0.00839514
0.0239909 0.857983 0.165531
-0.0267356 -0.246378 0.72953
Offset = [0.455821, 2.85223, 6.54556]
Background level guess :
first place: 0 (99.9101%)
second place: 51 (0.00201513%)
Guessed background level: 0
[AtlasCreator 05:06:22] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 05:06:31] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 05:06:31] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG7.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG7.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG7.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
285 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 210
LowHigh Thresholds: [0,77.5625,210]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0xe45a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4084
Debug: Off
Observers:
none
Matrix:
0.99863 -0.0511923 0.0108813
0.052336 0.976807 -0.207627
-8.67362e-19 0.207912 0.978148
Offset: [0.143583, 4.48321, 16.4234]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-0.0386671, 0.687888, 17.5538]
Inverse:
0.99863 0.052336 -8.67362e-19
-0.0511923 0.976807 0.207912
0.0108813 -0.207627 0.978148
Singular: 0
Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.999464 -0.022033 -0.0242268
0.017942 0.98732 -0.157728
0.0273948 0.157208 0.987185
Offset = [0.732292, 3.33512, 16.781]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.873645 -0.0189122 -0.0447535
0.0151449 0.886858 -0.0830694
0.0461646 0.0822935 0.728547
Offset = [0.318008, 2.97538, 22.4698]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.874348 -0.0189924 -0.0417969
0.00834498 0.882129 -0.109838
0.0383251 0.0752491 0.729811
Offset = [0.396177, 3.31913, 22.4837]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.877349 -0.020065 -0.0394302
0.0164631 0.883227 -0.112114
0.031451 0.0742426 0.728164
Offset = [0.568318, 3.36263, 22.2483]
Guessed background level: 0
[AtlasCreator 05:10:30] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 05:10:39] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 05:10:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
288 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 193
LowHigh Thresholds: [0,71.3672,193]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x1507a50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4075
Debug: Off
Observers:
none
Matrix:
0.994522 0.103956 -0.0109262
-0.104528 0.989074 -0.103956
-8.67362e-19 0.104528 0.994522
Offset: [0.208235, 1.48866, 11.0222]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [0.782078, -0.200541, 11.6846]
Inverse:
0.994522 -0.104528 -8.67362e-19
0.103956 0.989074 0.104528
-0.0109262 -0.103956 0.994522
Singular: 0
Versor: [ 0.0522642, -0.00273905, -0.0522642, 0.997261 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.99631 0.085704 -0.00454904
-0.0858244 0.994807 -0.0547041
-0.000162938 0.0548927 0.998492
Offset = [-0.152147, 0.231535, 11.9026]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 321 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.830154 0.0633601 -0.0123369
-0.0637634 0.880341 -0.035623
0.0100468 0.0363353 0.708667
Offset = [-0.433452, 0.872768, 18.6895]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.825148 0.0639851 -0.0244407
-0.0312094 0.876738 -0.0849879
-0.000259088 0.0140189 0.701251
Offset = [0.00771976, 1.62609, 18.319]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.820191 0.0668998 -0.02416
-0.0295308 0.87552 -0.0781942
-0.00207584 0.0121068 0.690591
Offset = [0.00520848, 1.53954, 18.3853]
Guessed background level: 0
[AtlasCreator 05:15:48] DEBUG: Guessing background value: 0.0
Background level guess :
first place: 0 (96.0151%)
second place: 0 (0.0284443%)
Guessed background level: 0
[AtlasCreator 05:15:57] DEBUG: Guessing background value for template: 0.0
[AtlasCreator 05:15:57] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG9.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG9.mat --outputVolume /var/tmp/haehn/Slicer3haehn/oGGeerAtlasCreator/caseG9.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5
Original Fixed image origin[-120, 93, 120, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleVersor3D(2 of 4).
TranformTypes: ScaleSkewVersor3D(3 of 4).
TranformTypes: Affine(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
305 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 198
LowHigh Thresholds: [0,70.8906,198]
maxSIDirection = 120
Computing Sampled Distance Computations
ListSample TotalFrequency is 8126464
188 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 177
LowHigh Thresholds: [0,67.5409,177]
maxSIDirection = 120
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x158aa50)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 4072
Debug: Off
Observers:
none
Matrix:
0.99863 0.0511923 0.0108813
-0.052336 0.976807 0.207627
-8.67362e-19 -0.207912 0.978148
Offset: [-1.6712, -3.72341, 14.2956]
Center: [-1.5765, 7.23158, 17.0743]
Translation: [-1.11305, -0.263539, 12.419]
Inverse:
0.99863 -0.052336 -8.67362e-19
0.0511923 0.976807 -0.207912
0.0108813 0.207627 0.978148
Singular: 0
Versor: [ -0.104493, 0.00273624, -0.0260335, 0.994181 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.998753 0.0347875 -0.0358057
-0.0285622 0.986431 0.161674
0.0409441 -0.16045 0.986194
Offset = [-0.535435, -2.94576, 13.9172]
=============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 137 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.871616 0.0114035 -0.0600889
-0.00352748 0.839172 0.129582
0.0610596 -0.129127 0.731097
Offset = [-0.727328, -0.583716, 19.0809]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.873571 0.0154404 -0.060369
0.0311819 0.836118 0.0664666
0.0443795 -0.15501 0.725888
Offset = [-0.787054, 0.526078, 18.8377]
=============================== Starting Transform Estimations for Affine(4 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.870606 0.0114926 -0.0556033
0.0340665 0.83481 0.053081
0.0391894 -0.14737 0.72601
Offset = [-0.842721, 0.328643, 18.8279]
[AtlasCreator 05:20:09] Waiting for Registration to complete..
[AtlasCreator 05:20:14] DEBUG: All outputs exist!
[AtlasCreator 05:20:14] End of Dynamic registration..
[AtlasCreator 05:20:22] Saving template to /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/template.nrrd
[AtlasCreator 05:20:24] Entering Resampling Stage..
[AtlasCreator 05:20:24] Found 3D Slicer launcher at /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3
[AtlasCreator 05:20:24] DEBUG: The launchCommandPrefix is /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/
Guessed background level: 0
[AtlasCreator 05:20:33] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:20:33] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case10.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case10.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case10.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case10.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case10.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case10.mat
Guessed background level: 0
[AtlasCreator 05:20:47] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:20:47] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case12.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case12.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case12.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case12.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case12.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case12.mat
Guessed background level: 0
[AtlasCreator 05:20:59] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:20:59] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case14.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case14.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case14.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case14.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case14.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case14.mat
Guessed background level: 0
[AtlasCreator 05:21:11] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:21:11] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case15.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case15.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case15.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case15.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case15.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case15.mat
Guessed background level: 0
[AtlasCreator 05:21:23] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:21:23] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case19.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case19.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case19.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case19.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case19.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case19.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case19.mat
Guessed background level: 0
[AtlasCreator 05:21:38] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:21:38] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case2.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case2.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case2.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case2.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case2.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case2.mat
Guessed background level: 0
[AtlasCreator 05:21:50] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:21:50] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case20.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case20.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case20.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case20.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case20.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case20.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case20.mat
Guessed background level: 0
[AtlasCreator 05:22:02] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:22:02] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case23.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case23.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case23.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case23.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case23.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case23.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case23.mat
Guessed background level: 0
[AtlasCreator 05:22:14] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:22:14] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case26.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case26.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case26.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case26.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case26.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case26.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case26.mat
Guessed background level: 0
[AtlasCreator 05:22:26] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:22:26] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case27.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case27.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case27.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case27.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case27.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case27.mat
Guessed background level: 0
[AtlasCreator 05:22:38] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:22:38] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case29.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case29.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case29.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case29.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case29.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case29.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case29.mat
Guessed background level: 0
[AtlasCreator 05:22:51] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:22:51] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case3.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case3.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case3.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case3.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case3.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case3.mat
Guessed background level: 0
[AtlasCreator 05:23:04] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:23:04] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case32.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case32.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case32.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case32.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case32.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case32.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case32.mat
Guessed background level: 0
[AtlasCreator 05:23:18] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:23:18] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case33.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case33.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case33.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case33.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case33.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case33.mat
Guessed background level: 0
[AtlasCreator 05:23:30] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:23:30] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case36.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case36.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case36.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case36.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case36.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case36.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case36.mat
Guessed background level: 0
[AtlasCreator 05:23:43] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:23:43] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case40.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case40.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case40.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case40.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case40.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case40.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case40.mat
Guessed background level: 0
[AtlasCreator 05:23:56] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:23:56] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case41.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case41.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case41.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case41.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case41.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case41.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case41.mat
Guessed background level: 0
[AtlasCreator 05:24:09] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:24:09] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case42.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case42.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case42.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case42.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case42.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case42.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case42.mat
Guessed background level: 0
[AtlasCreator 05:24:21] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:24:21] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case46.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case46.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case46.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case46.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case46.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case46.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case46.mat
Guessed background level: 0
[AtlasCreator 05:24:34] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:24:34] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case47.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case47.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case47.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case47.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case47.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case47.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case47.mat
Guessed background level: 0
[AtlasCreator 05:24:46] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:24:46] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case48.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case48.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case48.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case48.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case48.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case48.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case48.mat
Guessed background level: 0
[AtlasCreator 05:24:59] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:24:59] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case5.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case5.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case5.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case5.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case5.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case5.mat
Guessed background level: 0
[AtlasCreator 05:25:12] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:25:12] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case51.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case51.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case51.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case51.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case51.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case51.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case51.mat
Guessed background level: 0
[AtlasCreator 05:25:24] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:25:24] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case53.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case53.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case53.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case53.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case53.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case53.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case53.mat
Guessed background level: 0
[AtlasCreator 05:25:37] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:25:37] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case54.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case54.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case54.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case54.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case54.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case54.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case54.mat
Guessed background level: 0
[AtlasCreator 05:25:50] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:25:50] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case57.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case57.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case57.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case57.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case57.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case57.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case57.mat
Guessed background level: 0
[AtlasCreator 05:26:03] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:26:03] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case59.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case59.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case59.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case59.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case59.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case59.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case59.mat
Guessed background level: 0
[AtlasCreator 05:26:15] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:26:15] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case60.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case60.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case60.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case60.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case60.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case60.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case60.mat
Guessed background level: 0
[AtlasCreator 05:26:28] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:26:28] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case61.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case61.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case61.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case61.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case61.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case61.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case61.mat
Guessed background level: 0
[AtlasCreator 05:26:41] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:26:41] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case62.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case62.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case62.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case62.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case62.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case62.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case62.mat
Guessed background level: 0
[AtlasCreator 05:26:54] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:26:54] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case8.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case8.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case8.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/case8.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case8.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/case8.mat
Guessed background level: 0
[AtlasCreator 05:27:08] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:27:08] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG1.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG1.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG1.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG1.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG1.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG1.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG1.mat
Guessed background level: 0
[AtlasCreator 05:27:20] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:27:20] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG10.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG10.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG10.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG10.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG10.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG10.mat
Guessed background level: 0
[AtlasCreator 05:27:33] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:27:33] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG11.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG11.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG11.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG11.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG11.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG11.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG11.mat
Guessed background level: 0
[AtlasCreator 05:27:46] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:27:46] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG12.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG12.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG12.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG12.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG12.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG12.mat
Guessed background level: 0
[AtlasCreator 05:27:59] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:27:59] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG13.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG13.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG13.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG13.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG13.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG13.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG13.mat
Guessed background level: 0
[AtlasCreator 05:28:12] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:28:12] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG14.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG14.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG14.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG14.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG14.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG14.mat
Guessed background level: 0
[AtlasCreator 05:28:26] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:28:26] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG15.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG15.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG15.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG15.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG15.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG15.mat
Guessed background level: 0
[AtlasCreator 05:28:39] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:28:39] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG16.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG16.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG16.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG16.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG16.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG16.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG16.mat
Guessed background level: 0
[AtlasCreator 05:28:53] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:28:53] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG17.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG17.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG17.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG17.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG17.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG17.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG17.mat
Guessed background level: 0
[AtlasCreator 05:29:07] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:29:07] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG2.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG2.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG2.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG2.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG2.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG2.mat
Guessed background level: 0
[AtlasCreator 05:29:21] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:29:21] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG27.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG27.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG27.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG27.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG27.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG27.mat
Guessed background level: 0
[AtlasCreator 05:29:35] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:29:35] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG3.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG3.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG3.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG3.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG3.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG3.mat
Guessed background level: 0
[AtlasCreator 05:29:49] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:29:49] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG33.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG33.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG33.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG33.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG33.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG33.mat
Guessed background level: 0
[AtlasCreator 05:30:02] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:30:02] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG4.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG4.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG4.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG4.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG4.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG4.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG4.mat
Guessed background level: 0
[AtlasCreator 05:30:16] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:30:16] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG5.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG5.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG5.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG5.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG5.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG5.mat
Guessed background level: 0
[AtlasCreator 05:30:29] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:30:29] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG6.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG6.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG6.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG6.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG6.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG6.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG6.mat
Guessed background level: 0
[AtlasCreator 05:30:43] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:30:43] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG7.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG7.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG7.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG7.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG7.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG7.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG7.mat
Guessed background level: 0
[AtlasCreator 05:30:58] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:30:58] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG8.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG8.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG8.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG8.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG8.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG8.mat
Guessed background level: 0
[AtlasCreator 05:31:12] DEBUG: Guessing background value: 0.0
[AtlasCreator 05:31:12] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG9.nrrd --referenceVolume /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG9.mat --outputVolume /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG9.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor
=====================================================
Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG9.nrrd
Reference Volume: /var/tmp/haehn/Slicer3haehn/tmpMeanImage.nrrd
Output Volume: /var/tmp/haehn/Slicer3haehn/VaCewSAtlasCreatorResampled/caseG9.nrrd
Pixel Type: short
Interpolation: NearestNeighbor
Background Value: 0
Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG9.mat
=====================================================
Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitDynamic/caseG9.mat
[AtlasCreator 05:31:17] Entering Combine-To-Atlas Stage..
[AtlasCreator 05:40:23] Re-Casting atlas for label 32 to Short
[AtlasCreator 05:50:58] Re-Casting atlas for label 3 to Short
[AtlasCreator 06:03:08] Re-Casting atlas for label 4 to Short
[AtlasCreator 06:17:04] Re-Casting atlas for label 5 to Short
[AtlasCreator 06:33:06] Re-Casting atlas for label 6 to Short
[AtlasCreator 06:51:22] Re-Casting atlas for label 7 to Short
[AtlasCreator 07:12:05] Re-Casting atlas for label 8 to Short
[AtlasCreator 07:35:32] Re-Casting atlas for label 9 to Short
[AtlasCreator 08:01:54] Re-Casting atlas for label 10 to Short
[AtlasCreator 08:31:26] Re-Casting atlas for label 31 to Short
[AtlasCreator 08:31:27] Re-Casting atlas to Short
[AtlasCreator 08:31:30] --------------------------------------------------------------------------------
[AtlasCreator 08:31:30] All Done, folks!
[AtlasCreator 08:31:30] --------------------------------------------------------------------------------
Generic Warning: In /var/tmp/haehn/SLICER/TRUNK/Slicer3-lib/VTK/Common/vtkDebugLeaks.cxx, line 296
Deleting unknown object: vtkSlicerApplication