14:20:11 daniel@sbia-pc66:~/SLICER/TRUNK/Slicer3/Modules/AtlasCreator$ python atlascreator.py -i /Users/daniel/Desktop/ATLASCREATORTEST/originals/ -s /Users/daniel/Desktop/ATLASCREATORTEST/segmentations -o /Users/daniel/Desktop/ATLASCREATORTEST/ --dynamic --meanIterations 2 -w -l "3 4 5 6 7 8 9 10 31 32" --cmtk --debug --keepAligned
AtlasCreator for 3D Slicer
Version v0.2
Found 3D Slicer3 launcher at /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3
Warning: The output directory (/Users/daniel/Desktop/ATLASCREATORTEST) already exists..
Warning: Using new output directory instead: /Users/daniel/Desktop/ATLASCREATORTEST4
Debug Mode is enabled!
Adding module path: /Users/daniel/Downloads/Dumb/lib/Slicer3/Plugins:/Users/daniel/Slicer3daniel/16106/CMTK4Slicer
Starting Slicer: /Users/daniel/SLICER/TRUNK/Slicer3-build
[AtlasCreator 14:20:38] --------------------------------------------------------------------------------
[AtlasCreator 14:20:38] Starting Atlas Creator Normal Mode
[AtlasCreator 14:20:38] DEBUG: Looking for CMTK in /Users/daniel/Slicer3daniel/16106
[AtlasCreator 14:20:38] Found CMTK at: /Users/daniel/Slicer3daniel/16106/CMTK4Slicer
[AtlasCreator 14:20:38] Configuration for Atlas Creator:
Original Images: ['/Users/daniel/Desktop/ATLASCREATORTEST/originals/case10.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case12.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case2.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case3.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case5.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case8.nrrd']
Segmentations: ['/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case10.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case12.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case2.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case3.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case5.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case8.nrrd']
Output Directory: /Users/daniel/Desktop/ATLASCREATORTEST4/
Template Type: dynamic
Dynamic Template Iterations: 2
Fixed Template Default Case:
Labels: [32, 3, 4, 5, 6, 7, 8, 9, 10, 31]
Toolkit: CMTK
Registration Type: Affine
Save Transforms: 1
Delete Aligned Images: 0
Delete Aligned Segmentations: 0
Normalize Atlases: 0
Output Cast: Short
[AtlasCreator 14:20:38] Entering Registration Stage..
[AtlasCreator 14:20:38] Found 3D Slicer launcher at /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3
[AtlasCreator 14:20:38] DEBUG: Looking for CMTK in /Users/daniel/Slicer3daniel/16106
[AtlasCreator 14:20:38] DEBUG: The launchCommandPrefix is /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/
[AtlasCreator 14:20:38] Dynamic registration with 2 iterations
[AtlasCreator 14:20:38] Starting iteration 1...
Background level guess :
first place: 4 (11.4145%)
second place: 5 (11.2047%)
Guessed background level: 4
[AtlasCreator 14:20:51] DEBUG: Guessing background value: 4.0
Background level guess :
first place: 4 (3.15972%)
second place: 4 (2.98913%)
Guessed background level: 4.5
[AtlasCreator 14:20:53] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:20:53] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case10.mat --pad-ref 4.5 --pad-flt 4.0 --write-reformatted /Users/daniel/Slicer3daniel/G9XIJHAtlasCreator/case10.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case10.nrrd
AffineImageRegistration
"AffineImageRegistration"
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0.05
0.1
0.15
0.2
0
0.05
0.1
0.15
0.2
0.25
0.25
0.3125
0.375
0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
0.5
0.583333
0.666667
0.75
0.75
0.875
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0.875
1
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0.00390625
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0.148438
0.152344
0.15625
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0.183594
0.1875
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0.21875
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0.25
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0.390625
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0.398438
0.402344
0.40625
0.410156
0.414062
0.417969
0.421875
0.425781
0.429688
0.433594
0.4375
0.441406
0.445312
0.449219
0.453125
0.457031
0.460938
0.464844
0.46875
0.472656
0.476562
0.480469
0.484375
0.488281
0.492188
0.496094
0.5
0.503906
0.507812
0.511719
0.515625
0.519531
0.523438
0.527344
0.53125
0.535156
0.539062
0.542969
0.546875
0.550781
0.554688
0.558594
0.5625
0.566406
0.570312
0.574219
0.578125
0.582031
0.585938
0.589844
0.59375
0.597656
0.601562
0.605469
0.609375
0.613281
0.617188
0.621094
0.625
0.628906
0.632812
0.636719
0.640625
0.644531
0.648438
0.652344
0.65625
0.660156
0.664062
0.667969
0.671875
0.675781
0.679688
0.683594
0.6875
0.691406
0.695312
0.699219
0.703125
0.707031
0.710938
0.714844
0.71875
0.722656
0.726562
0.730469
0.734375
0.738281
0.742188
0.746094
0.75
0.753906
0.757812
0.761719
0.765625
0.769531
0.773438
0.777344
0.78125
0.785156
0.789062
0.792969
0.796875
0.800781
0.804688
0.808594
0.8125
0.816406
0.820312
0.824219
0.828125
0.832031
0.835938
0.839844
0.84375
0.847656
0.851562
0.855469
0.859375
0.863281
0.867188
0.871094
0.875
0.878906
0.882812
0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
0.910156
0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
0.964844
0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
15
Background level guess :
first place: 3 (19.7612%)
second place: 4 (17.1901%)
Guessed background level: 3
[AtlasCreator 14:22:47] DEBUG: Guessing background value: 3.0
Background level guess :
first place: 4 (3.15972%)
second place: 4 (2.98913%)
Guessed background level: 4.5
[AtlasCreator 14:22:49] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:22:49] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case12.mat --pad-ref 4.5 --pad-flt 3.0 --write-reformatted /Users/daniel/Slicer3daniel/G9XIJHAtlasCreator/case12.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case12.nrrd
AffineImageRegistration
"AffineImageRegistration"
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0.05
0.1
0.15
0.2
0
0.05
0.1
0.15
0.2
0.25
0.25
0.3125
0.375
0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
0.5
0.583333
0.666667
0.75
0.75
0.875
0.75
0.875
1
0
0.00390625
0.0078125
0.0117188
0.015625
0.0195312
0.0234375
0.0273438
0.03125
0.0351562
0.0390625
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0.046875
0.0507812
0.0546875
0.0585938
0.0625
0.0664062
0.0703125
0.0742188
0.078125
0.0820312
0.0859375
0.0898438
0.09375
0.0976562
0.101562
0.105469
0.109375
0.113281
0.117188
0.121094
0.125
0.128906
0.132812
0.136719
0.140625
0.144531
0.148438
0.152344
0.15625
0.160156
0.164062
0.167969
0.171875
0.175781
0.179688
0.183594
0.1875
0.191406
0.195312
0.199219
0.203125
0.207031
0.210938
0.214844
0.21875
0.222656
0.226562
0.230469
0.234375
0.238281
0.242188
0.246094
0.25
0.253906
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0.265625
0.269531
0.273438
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0.367188
0.371094
0.375
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0.402344
0.40625
0.410156
0.414062
0.417969
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0.433594
0.4375
0.441406
0.445312
0.449219
0.453125
0.457031
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0.464844
0.46875
0.472656
0.476562
0.480469
0.484375
0.488281
0.492188
0.496094
0.5
0.503906
0.507812
0.511719
0.515625
0.519531
0.523438
0.527344
0.53125
0.535156
0.539062
0.542969
0.546875
0.550781
0.554688
0.558594
0.5625
0.566406
0.570312
0.574219
0.578125
0.582031
0.585938
0.589844
0.59375
0.597656
0.601562
0.605469
0.609375
0.613281
0.617188
0.621094
0.625
0.628906
0.632812
0.636719
0.640625
0.644531
0.648438
0.652344
0.65625
0.660156
0.664062
0.667969
0.671875
0.675781
0.679688
0.683594
0.6875
0.691406
0.695312
0.699219
0.703125
0.707031
0.710938
0.714844
0.71875
0.722656
0.726562
0.730469
0.734375
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0.742188
0.746094
0.75
0.753906
0.757812
0.761719
0.765625
0.769531
0.773438
0.777344
0.78125
0.785156
0.789062
0.792969
0.796875
0.800781
0.804688
0.808594
0.8125
0.816406
0.820312
0.824219
0.828125
0.832031
0.835938
0.839844
0.84375
0.847656
0.851562
0.855469
0.859375
0.863281
0.867188
0.871094
0.875
0.878906
0.882812
0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
0.910156
0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
0.964844
0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
20.98
Background level guess :
first place: 2 (12.1833%)
second place: 3 (11.7794%)
Guessed background level: 2
[AtlasCreator 14:27:03] DEBUG: Guessing background value: 2.0
Background level guess :
first place: 4 (3.15972%)
second place: 4 (2.98913%)
Guessed background level: 4.5
[AtlasCreator 14:27:04] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:27:04] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case2.mat --pad-ref 4.5 --pad-flt 2.0 --write-reformatted /Users/daniel/Slicer3daniel/G9XIJHAtlasCreator/case2.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case2.nrrd
AffineImageRegistration
"AffineImageRegistration"
0
0.05
0.1
0.15
0.2
0
0.05
0.1
0.15
0.2
0.25
0.25
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0.375
0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
0.5
0.583333
0.666667
0.75
0.75
0.875
0.75
0.875
1
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0.00390625
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0.03125
0.0351562
0.0390625
0.0429688
0.046875
0.0507812
0.0546875
0.0585938
0.0625
0.0664062
0.0703125
0.0742188
0.078125
0.0820312
0.0859375
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0.113281
0.117188
0.121094
0.125
0.128906
0.132812
0.136719
0.140625
0.144531
0.148438
0.152344
0.15625
0.160156
0.164062
0.167969
0.171875
0.175781
0.179688
0.183594
0.1875
0.191406
0.195312
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0.203125
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0.214844
0.21875
0.222656
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0.230469
0.234375
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0.269531
0.273438
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0.296875
0.300781
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0.328125
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0.335938
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0.355469
0.359375
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0.367188
0.371094
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0.402344
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0.414062
0.417969
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0.425781
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0.433594
0.4375
0.441406
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0.449219
0.453125
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0.464844
0.46875
0.472656
0.476562
0.480469
0.484375
0.488281
0.492188
0.496094
0.5
0.503906
0.507812
0.511719
0.515625
0.519531
0.523438
0.527344
0.53125
0.535156
0.539062
0.542969
0.546875
0.550781
0.554688
0.558594
0.5625
0.566406
0.570312
0.574219
0.578125
0.582031
0.585938
0.589844
0.59375
0.597656
0.601562
0.605469
0.609375
0.613281
0.617188
0.621094
0.625
0.628906
0.632812
0.636719
0.640625
0.644531
0.648438
0.652344
0.65625
0.660156
0.664062
0.667969
0.671875
0.675781
0.679688
0.683594
0.6875
0.691406
0.695312
0.699219
0.703125
0.707031
0.710938
0.714844
0.71875
0.722656
0.726562
0.730469
0.734375
0.738281
0.742188
0.746094
0.75
0.753906
0.757812
0.761719
0.765625
0.769531
0.773438
0.777344
0.78125
0.785156
0.789062
0.792969
0.796875
0.800781
0.804688
0.808594
0.8125
0.816406
0.820312
0.824219
0.828125
0.832031
0.835938
0.839844
0.84375
0.847656
0.851562
0.855469
0.859375
0.863281
0.867188
0.871094
0.875
0.878906
0.882812
0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
0.910156
0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
0.964844
0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
20.52
Background level guess :
first place: 3 (20.7696%)
second place: 4 (17.3754%)
Guessed background level: 3
[AtlasCreator 14:29:40] DEBUG: Guessing background value: 3.0
Background level guess :
first place: 4 (3.15972%)
second place: 4 (2.98913%)
Guessed background level: 4.5
[AtlasCreator 14:29:41] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:29:41] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case3.mat --pad-ref 4.5 --pad-flt 3.0 --write-reformatted /Users/daniel/Slicer3daniel/G9XIJHAtlasCreator/case3.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case3.nrrd
AffineImageRegistration
"AffineImageRegistration"
0
0.05
0.1
0.15
0.2
0
0.05
0.1
0.15
0.2
0.25
0.25
0.3125
0.375
0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
0.5
0.583333
0.666667
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0.777344
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0.84375
0.847656
0.851562
0.855469
0.859375
0.863281
0.867188
0.871094
0.875
0.878906
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0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
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0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
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0.945312
0.949219
0.953125
0.957031
0.960938
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0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
20.42
Background level guess :
first place: 3 (19.8423%)
second place: 4 (17.4266%)
Guessed background level: 3
[AtlasCreator 14:32:29] DEBUG: Guessing background value: 3.0
Background level guess :
first place: 4 (3.15972%)
second place: 4 (2.98913%)
Guessed background level: 4.5
[AtlasCreator 14:32:30] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:32:30] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case5.mat --pad-ref 4.5 --pad-flt 3.0 --write-reformatted /Users/daniel/Slicer3daniel/G9XIJHAtlasCreator/case5.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case5.nrrd
AffineImageRegistration
"AffineImageRegistration"
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0.875
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0.902344
0.90625
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0.921875
0.925781
0.929688
0.933594
0.9375
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0.949219
0.953125
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0.960938
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0.992188
0.996094
AffineImageRegistration
21.75
Background level guess :
first place: 2 (11.5244%)
second place: 3 (11.1119%)
Guessed background level: 2
[AtlasCreator 14:34:47] DEBUG: Guessing background value: 2.0
Background level guess :
first place: 4 (3.15972%)
second place: 4 (2.98913%)
Guessed background level: 4.5
[AtlasCreator 14:34:48] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:34:48] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case8.mat --pad-ref 4.5 --pad-flt 2.0 --write-reformatted /Users/daniel/Slicer3daniel/G9XIJHAtlasCreator/case8.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case8.nrrd
AffineImageRegistration
"AffineImageRegistration"
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0.15
0.2
0
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0.15
0.2
0.25
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0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
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0.75
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0.8125
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0.828125
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0.84375
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0.859375
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0.867188
0.871094
0.875
0.878906
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0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
0.910156
0.914062
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0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
0.964844
0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
17.81
[AtlasCreator 14:37:24] Waiting for Registration to complete..
[AtlasCreator 14:37:29] DEBUG: All outputs exist!
[AtlasCreator 14:37:29] Starting iteration 2...
Warning: In /Users/daniel/SLICER/TRUNK/Slicer3/Libs/MRML/vtkMRMLVolumeArchetypeStorageNode.cxx, line 478
vtkMRMLVolumeArchetypeStorageNode (0x13a1e0c40): WriteData: removing old version of file /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd
Background level guess :
first place: 4 (11.4145%)
second place: 5 (11.2047%)
Guessed background level: 4
[AtlasCreator 14:37:41] DEBUG: Guessing background value: 4.0
Background level guess :
first place: 4 (3.39999%)
second place: 5 (2.88365%)
Guessed background level: 4.5
[AtlasCreator 14:37:43] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:37:43] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case10.mat --pad-ref 4.5 --pad-flt 4.0 --write-reformatted /Users/daniel/Slicer3daniel/iWoLsQAtlasCreator/case10.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case10.nrrd
AffineImageRegistration
"AffineImageRegistration"
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0.796875
0.800781
0.804688
0.808594
0.8125
0.816406
0.820312
0.824219
0.828125
0.832031
0.835938
0.839844
0.84375
0.847656
0.851562
0.855469
0.859375
0.863281
0.867188
0.871094
0.875
0.878906
0.882812
0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
0.910156
0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
0.964844
0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
15.06
Background level guess :
first place: 3 (19.7612%)
second place: 4 (17.1901%)
Guessed background level: 3
[AtlasCreator 14:40:26] DEBUG: Guessing background value: 3.0
Background level guess :
first place: 4 (3.39999%)
second place: 5 (2.88365%)
Guessed background level: 4.5
[AtlasCreator 14:40:27] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:40:27] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case12.mat --pad-ref 4.5 --pad-flt 3.0 --write-reformatted /Users/daniel/Slicer3daniel/iWoLsQAtlasCreator/case12.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case12.nrrd
AffineImageRegistration
"AffineImageRegistration"
0
0.05
0.1
0.15
0.2
0
0.05
0.1
0.15
0.2
0.25
0.25
0.3125
0.375
0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
0.5
0.583333
0.666667
0.75
0.75
0.875
0.75
0.875
1
0
0.00390625
0.0078125
0.0117188
0.015625
0.0195312
0.0234375
0.0273438
0.03125
0.0351562
0.0390625
0.0429688
0.046875
0.0507812
0.0546875
0.0585938
0.0625
0.0664062
0.0703125
0.0742188
0.078125
0.0820312
0.0859375
0.0898438
0.09375
0.0976562
0.101562
0.105469
0.109375
0.113281
0.117188
0.121094
0.125
0.128906
0.132812
0.136719
0.140625
0.144531
0.148438
0.152344
0.15625
0.160156
0.164062
0.167969
0.171875
0.175781
0.179688
0.183594
0.1875
0.191406
0.195312
0.199219
0.203125
0.207031
0.210938
0.214844
0.21875
0.222656
0.226562
0.230469
0.234375
0.238281
0.242188
0.246094
0.25
0.253906
0.257812
0.261719
0.265625
0.269531
0.273438
0.277344
0.28125
0.285156
0.289062
0.292969
0.296875
0.300781
0.304688
0.308594
0.3125
0.316406
0.320312
0.324219
0.328125
0.332031
0.335938
0.339844
0.34375
0.347656
0.351562
0.355469
0.359375
0.363281
0.367188
0.371094
0.375
0.378906
0.382812
0.386719
0.390625
0.394531
0.398438
0.402344
0.40625
0.410156
0.414062
0.417969
0.421875
0.425781
0.429688
0.433594
0.4375
0.441406
0.445312
0.449219
0.453125
0.457031
0.460938
0.464844
0.46875
0.472656
0.476562
0.480469
0.484375
0.488281
0.492188
0.496094
0.5
0.503906
0.507812
0.511719
0.515625
0.519531
0.523438
0.527344
0.53125
0.535156
0.539062
0.542969
0.546875
0.550781
0.554688
0.558594
0.5625
0.566406
0.570312
0.574219
0.578125
0.582031
0.585938
0.589844
0.59375
0.597656
0.601562
0.605469
0.609375
0.613281
0.617188
0.621094
0.625
0.628906
0.632812
0.636719
0.640625
0.644531
0.648438
0.652344
0.65625
0.660156
0.664062
0.667969
0.671875
0.675781
0.679688
0.683594
0.6875
0.691406
0.695312
0.699219
0.703125
0.707031
0.710938
0.714844
0.71875
0.722656
0.726562
0.730469
0.734375
0.738281
0.742188
0.746094
0.75
0.753906
0.757812
0.761719
0.765625
0.769531
0.773438
0.777344
0.78125
0.785156
0.789062
0.792969
0.796875
0.800781
0.804688
0.808594
0.8125
0.816406
0.820312
0.824219
0.828125
0.832031
0.835938
0.839844
0.84375
0.847656
0.851562
0.855469
0.859375
0.863281
0.867188
0.871094
0.875
0.878906
0.882812
0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
0.910156
0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
0.964844
0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
20.83
Background level guess :
first place: 2 (12.1833%)
second place: 3 (11.7794%)
Guessed background level: 2
[AtlasCreator 14:43:50] DEBUG: Guessing background value: 2.0
Background level guess :
first place: 4 (3.39999%)
second place: 5 (2.88365%)
Guessed background level: 4.5
[AtlasCreator 14:43:51] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:43:51] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case2.mat --pad-ref 4.5 --pad-flt 2.0 --write-reformatted /Users/daniel/Slicer3daniel/iWoLsQAtlasCreator/case2.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case2.nrrd
AffineImageRegistration
"AffineImageRegistration"
0
0.05
0.1
0.15
0.2
0
0.05
0.1
0.15
0.2
0.25
0.25
0.3125
0.375
0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
0.5
0.583333
0.666667
0.75
0.75
0.875
0.75
0.875
1
0
0.00390625
0.0078125
0.0117188
0.015625
0.0195312
0.0234375
0.0273438
0.03125
0.0351562
0.0390625
0.0429688
0.046875
0.0507812
0.0546875
0.0585938
0.0625
0.0664062
0.0703125
0.0742188
0.078125
0.0820312
0.0859375
0.0898438
0.09375
0.0976562
0.101562
0.105469
0.109375
0.113281
0.117188
0.121094
0.125
0.128906
0.132812
0.136719
0.140625
0.144531
0.148438
0.152344
0.15625
0.160156
0.164062
0.167969
0.171875
0.175781
0.179688
0.183594
0.1875
0.191406
0.195312
0.199219
0.203125
0.207031
0.210938
0.214844
0.21875
0.222656
0.226562
0.230469
0.234375
0.238281
0.242188
0.246094
0.25
0.253906
0.257812
0.261719
0.265625
0.269531
0.273438
0.277344
0.28125
0.285156
0.289062
0.292969
0.296875
0.300781
0.304688
0.308594
0.3125
0.316406
0.320312
0.324219
0.328125
0.332031
0.335938
0.339844
0.34375
0.347656
0.351562
0.355469
0.359375
0.363281
0.367188
0.371094
0.375
0.378906
0.382812
0.386719
0.390625
0.394531
0.398438
0.402344
0.40625
0.410156
0.414062
0.417969
0.421875
0.425781
0.429688
0.433594
0.4375
0.441406
0.445312
0.449219
0.453125
0.457031
0.460938
0.464844
0.46875
0.472656
0.476562
0.480469
0.484375
0.488281
0.492188
0.496094
0.5
0.503906
0.507812
0.511719
0.515625
0.519531
0.523438
0.527344
0.53125
0.535156
0.539062
0.542969
0.546875
0.550781
0.554688
0.558594
0.5625
0.566406
0.570312
0.574219
0.578125
0.582031
0.585938
0.589844
0.59375
0.597656
0.601562
0.605469
0.609375
0.613281
0.617188
0.621094
0.625
0.628906
0.632812
0.636719
0.640625
0.644531
0.648438
0.652344
0.65625
0.660156
0.664062
0.667969
0.671875
0.675781
0.679688
0.683594
0.6875
0.691406
0.695312
0.699219
0.703125
0.707031
0.710938
0.714844
0.71875
0.722656
0.726562
0.730469
0.734375
0.738281
0.742188
0.746094
0.75
0.753906
0.757812
0.761719
0.765625
0.769531
0.773438
0.777344
0.78125
0.785156
0.789062
0.792969
0.796875
0.800781
0.804688
0.808594
0.8125
0.816406
0.820312
0.824219
0.828125
0.832031
0.835938
0.839844
0.84375
0.847656
0.851562
0.855469
0.859375
0.863281
0.867188
0.871094
0.875
0.878906
0.882812
0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
0.910156
0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
0.964844
0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
20.55
Background level guess :
first place: 3 (20.7696%)
second place: 4 (17.3754%)
Guessed background level: 3
[AtlasCreator 14:46:24] DEBUG: Guessing background value: 3.0
Background level guess :
first place: 4 (3.39999%)
second place: 5 (2.88365%)
Guessed background level: 4.5
[AtlasCreator 14:46:25] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:46:25] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case3.mat --pad-ref 4.5 --pad-flt 3.0 --write-reformatted /Users/daniel/Slicer3daniel/iWoLsQAtlasCreator/case3.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case3.nrrd
AffineImageRegistration
"AffineImageRegistration"
0
0.05
0.1
0.15
0.2
0
0.05
0.1
0.15
0.2
0.25
0.25
0.3125
0.375
0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
0.5
0.583333
0.666667
0.75
0.75
0.875
0.75
0.875
1
0
0.00390625
0.0078125
0.0117188
0.015625
0.0195312
0.0234375
0.0273438
0.03125
0.0351562
0.0390625
0.0429688
0.046875
0.0507812
0.0546875
0.0585938
0.0625
0.0664062
0.0703125
0.0742188
0.078125
0.0820312
0.0859375
0.0898438
0.09375
0.0976562
0.101562
0.105469
0.109375
0.113281
0.117188
0.121094
0.125
0.128906
0.132812
0.136719
0.140625
0.144531
0.148438
0.152344
0.15625
0.160156
0.164062
0.167969
0.171875
0.175781
0.179688
0.183594
0.1875
0.191406
0.195312
0.199219
0.203125
0.207031
0.210938
0.214844
0.21875
0.222656
0.226562
0.230469
0.234375
0.238281
0.242188
0.246094
0.25
0.253906
0.257812
0.261719
0.265625
0.269531
0.273438
0.277344
0.28125
0.285156
0.289062
0.292969
0.296875
0.300781
0.304688
0.308594
0.3125
0.316406
0.320312
0.324219
0.328125
0.332031
0.335938
0.339844
0.34375
0.347656
0.351562
0.355469
0.359375
0.363281
0.367188
0.371094
0.375
0.378906
0.382812
0.386719
0.390625
0.394531
0.398438
0.402344
0.40625
0.410156
0.414062
0.417969
0.421875
0.425781
0.429688
0.433594
0.4375
0.441406
0.445312
0.449219
0.453125
0.457031
0.460938
0.464844
0.46875
0.472656
0.476562
0.480469
0.484375
0.488281
0.492188
0.496094
0.5
0.503906
0.507812
0.511719
0.515625
0.519531
0.523438
0.527344
0.53125
0.535156
0.539062
0.542969
0.546875
0.550781
0.554688
0.558594
0.5625
0.566406
0.570312
0.574219
0.578125
0.582031
0.585938
0.589844
0.59375
0.597656
0.601562
0.605469
0.609375
0.613281
0.617188
0.621094
0.625
0.628906
0.632812
0.636719
0.640625
0.644531
0.648438
0.652344
0.65625
0.660156
0.664062
0.667969
0.671875
0.675781
0.679688
0.683594
0.6875
0.691406
0.695312
0.699219
0.703125
0.707031
0.710938
0.714844
0.71875
0.722656
0.726562
0.730469
0.734375
0.738281
0.742188
0.746094
0.75
0.753906
0.757812
0.761719
0.765625
0.769531
0.773438
0.777344
0.78125
0.785156
0.789062
0.792969
0.796875
0.800781
0.804688
0.808594
0.8125
0.816406
0.820312
0.824219
0.828125
0.832031
0.835938
0.839844
0.84375
0.847656
0.851562
0.855469
0.859375
0.863281
0.867188
0.871094
0.875
0.878906
0.882812
0.886719
0.890625
0.894531
0.898438
0.902344
0.90625
0.910156
0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
0.964844
0.96875
0.972656
0.976562
0.980469
0.984375
0.988281
0.992188
0.996094
AffineImageRegistration
20.45
Background level guess :
first place: 3 (19.8423%)
second place: 4 (17.4266%)
Guessed background level: 3
[AtlasCreator 14:50:20] DEBUG: Guessing background value: 3.0
Background level guess :
first place: 4 (3.39999%)
second place: 5 (2.88365%)
Guessed background level: 4.5
[AtlasCreator 14:50:21] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:50:21] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case5.mat --pad-ref 4.5 --pad-flt 3.0 --write-reformatted /Users/daniel/Slicer3daniel/iWoLsQAtlasCreator/case5.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case5.nrrd
AffineImageRegistration
"AffineImageRegistration"
0
0.05
0.1
0.15
0.2
0
0.05
0.1
0.15
0.2
0.25
0.25
0.3125
0.375
0.4375
0.25
0.3125
0.375
0.4375
0.5
0.5
0.583333
0.666667
0.5
0.583333
0.666667
0.75
0.75
0.875
0.75
0.875
1
0
0.00390625
0.0078125
0.0117188
0.015625
0.0195312
0.0234375
0.0273438
0.03125
0.0351562
0.0390625
0.0429688
0.046875
0.0507812
0.0546875
0.0585938
0.0625
0.0664062
0.0703125
0.0742188
0.078125
0.0820312
0.0859375
0.0898438
0.09375
0.0976562
0.101562
0.105469
0.109375
0.113281
0.117188
0.121094
0.125
0.128906
0.132812
0.136719
0.140625
0.144531
0.148438
0.152344
0.15625
0.160156
0.164062
0.167969
0.171875
0.175781
0.179688
0.183594
0.1875
0.191406
0.195312
0.199219
0.203125
0.207031
0.210938
0.214844
0.21875
0.222656
0.226562
0.230469
0.234375
0.238281
0.242188
0.246094
0.25
0.253906
0.257812
0.261719
0.265625
0.269531
0.273438
0.277344
0.28125
0.285156
0.289062
0.292969
0.296875
0.300781
0.304688
0.308594
0.3125
0.316406
0.320312
0.324219
0.328125
0.332031
0.335938
0.339844
0.34375
0.347656
0.351562
0.355469
0.359375
0.363281
0.367188
0.371094
0.375
0.378906
0.382812
0.386719
0.390625
0.394531
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0.871094
0.875
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0.886719
0.890625
0.894531
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0.902344
0.90625
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0.914062
0.917969
0.921875
0.925781
0.929688
0.933594
0.9375
0.941406
0.945312
0.949219
0.953125
0.957031
0.960938
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AffineImageRegistration
21.69
Background level guess :
first place: 2 (11.5244%)
second place: 3 (11.1119%)
Guessed background level: 2
[AtlasCreator 14:53:12] DEBUG: Guessing background value: 2.0
Background level guess :
first place: 4 (3.39999%)
second place: 5 (2.88365%)
Guessed background level: 4.5
[AtlasCreator 14:53:14] DEBUG: Guessing background value for template: 4.5
[AtlasCreator 14:53:14] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/registration --initxlate --exploration 8.0 --dofs 6 --dofs 9 --accuracy 0.5 -o /Users/daniel/Desktop/ATLASCREATORTEST4/case8.mat --pad-ref 4.5 --pad-flt 2.0 --write-reformatted /Users/daniel/Slicer3daniel/iWoLsQAtlasCreator/case8.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST/originals/case8.nrrd
AffineImageRegistration
"AffineImageRegistration"
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0.5
0.5
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1
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AffineImageRegistration
18.19
[AtlasCreator 14:56:47] Waiting for Registration to complete..
[AtlasCreator 14:56:52] DEBUG: All outputs exist!
[AtlasCreator 14:56:52] End of Dynamic registration..
[AtlasCreator 14:56:53] Saving template to /Users/daniel/Desktop/ATLASCREATORTEST4/template.nrrd
[AtlasCreator 14:57:02] Entering Resampling Stage..
[AtlasCreator 14:57:02] Found 3D Slicer launcher at /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3
[AtlasCreator 14:57:02] DEBUG: Looking for CMTK in /Users/daniel/Slicer3daniel/16106
[AtlasCreator 14:57:02] DEBUG: The launchCommandPrefix is /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/
Guessed background level: 0
[AtlasCreator 14:57:02] DEBUG: Guessing background value: 0.0
[AtlasCreator 14:57:02] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/reformatx -o /Users/daniel/Slicer3daniel/DjDCVZAtlasCreatorResampled/case10.nrrd --pad-out 0.0 --floating /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case10.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST4/case10.mat
""
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0.875
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0.90625
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7.46
Guessed background level: 0
[AtlasCreator 14:57:12] DEBUG: Guessing background value: 0.0
[AtlasCreator 14:57:12] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/reformatx -o /Users/daniel/Slicer3daniel/DjDCVZAtlasCreatorResampled/case12.nrrd --pad-out 0.0 --floating /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case12.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST4/case12.mat
""
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0.871094
0.875
0.878906
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0.894531
0.898438
0.902344
0.90625
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0.96875
0.972656
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0.980469
0.984375
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7.49
Guessed background level: 0
[AtlasCreator 14:57:22] DEBUG: Guessing background value: 0.0
[AtlasCreator 14:57:22] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/reformatx -o /Users/daniel/Slicer3daniel/DjDCVZAtlasCreatorResampled/case2.nrrd --pad-out 0.0 --floating /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case2.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST4/case2.mat
""
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Guessed background level: 0
[AtlasCreator 14:57:33] DEBUG: Guessing background value: 0.0
[AtlasCreator 14:57:33] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/reformatx -o /Users/daniel/Slicer3daniel/DjDCVZAtlasCreatorResampled/case3.nrrd --pad-out 0.0 --floating /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case3.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST4/case3.mat
""
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Guessed background level: 0
[AtlasCreator 14:57:43] DEBUG: Guessing background value: 0.0
[AtlasCreator 14:57:43] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/reformatx -o /Users/daniel/Slicer3daniel/DjDCVZAtlasCreatorResampled/case5.nrrd --pad-out 0.0 --floating /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case5.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST4/case5.mat
""
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Guessed background level: 0
[AtlasCreator 14:57:53] DEBUG: Guessing background value: 0.0
[AtlasCreator 14:57:53] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/Slicer3daniel/16106/CMTK4Slicer/reformatx -o /Users/daniel/Slicer3daniel/DjDCVZAtlasCreatorResampled/case8.nrrd --pad-out 0.0 --floating /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case8.nrrd /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd /Users/daniel/Desktop/ATLASCREATORTEST4/case8.mat
""
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[AtlasCreator 14:58:03] Entering Combine-To-Atlas Stage..
[AtlasCreator 14:58:05] Re-Casting atlas for label 32 to Short
[AtlasCreator 14:58:07] Re-Casting atlas for label 3 to Short
[AtlasCreator 14:58:09] Re-Casting atlas for label 4 to Short
[AtlasCreator 14:58:12] Re-Casting atlas for label 5 to Short
[AtlasCreator 14:58:14] Re-Casting atlas for label 6 to Short
[AtlasCreator 14:58:17] Re-Casting atlas for label 7 to Short
[AtlasCreator 14:58:19] Re-Casting atlas for label 8 to Short
[AtlasCreator 14:58:22] Re-Casting atlas for label 9 to Short
[AtlasCreator 14:58:25] Re-Casting atlas for label 10 to Short
[AtlasCreator 14:58:27] Re-Casting atlas for label 31 to Short
[AtlasCreator 14:58:28] Re-Casting atlas to Short
[AtlasCreator 14:58:28] --------------------------------------------------------------------------------
[AtlasCreator 14:58:28] All Done, folks!
[AtlasCreator 14:58:28] --------------------------------------------------------------------------------
Thread ID: -1