Projects:RegistrationLibrary:RegLib C37 - Revision history

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Registration Results

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2011-03-03T21:19:21Z

Procedures

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==v3.6.1 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #37: Intra-subject Brain MRI: T1 Tumor Growth / Resection Assessment==
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C37_Thumb1.png|200px|lleft|this is the fixed reference image. All images are aligned into this space]]
|[[Image:RegArrow_Affine.png|100px|lleft]]
|[[Image:RegLib_C37_Thumb1|200px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
|-
|fixed image/target
|
|moving image
|}

=== Modules ===
'''Slicer 3.6.1''' recommended modules:
*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]
*[http://www.slicer.org/slicerWiki/index.php/Modules:SkullStripperModule Skull-Stripper Module]

===Objective / Background ===
This is a typical case of change assessment.
=== Keywords ===
MRI, brain, head, intra-subject, T1, tumor, change assessment

===Input Data===
*reference/fixed : T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal
*moving: T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal

=== Registration Results===
{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C37_.gif|400px|center|Fast Affine registration result]]
|[[Image:RegLib01_GifAnim_reg.gif|200px|center|after orientation]]
|[[Image:RegLib01_ColorAnim.gif|200px|center|before/after registration, indiv. images in red/cyan, match in gray]]
|-
|''Fast Affine'' registration result
|''ExpertAutomatedRegistration'' registration result
|before/after registration with ''ExpertAutomatedRegistration'' module
|}

===Download ===
*Slicer 3.6.1 packages:
**'''[[Media:RegLib_C01_DATA.zip‎|Image Data + solutions package (Data, Solution, zip file qqMB) ]]'''
**'''[[Media:RegLib_C01_ScreenCast.mov|ScreenCast video (Quicktime movie 14MB) ]]'''
*Slicer 3.4 packages:
**[[Media:RegLib_Case_01_TumorGrowth.zip‎|download entire package (Data,Presets,Tutorial, Solution, zip file 33.7 MB) ]]
**[[Media:RegLib_Case_01_TumorGrowth.zip‎|download entire package (Data,Presets,Tutorial, Solution, zip file 33.7 MB) ]]
**[[Media:RegPreset_RegUC-001.txt|download registration parameter presets file (MRML file, import as scene) ]]
**[[Media:RegLib_C01_Data_TumorGrowth.zip|download image dataset only (NRRD, 10.7 MB, filename: RegLib_C01_Data_TumorGrowth.zip) ]]
**[[Media:RegLib_Case_01_NRRD_TumorGrowth.zip|download image dataset only (NRRD, 10.7 MB, filename: RegLib_Case_01_NRRD_TumorGrowth.zip) ]]
**[[Media:RegLib_C01_DataNIFTI_TumorGrowth.zip|download image dataset in NIFTI format (NIFTI / nii, 10.7 MB, filename: RegLib_C01_DataNIFTI_TumorGrowth.zip) ]]
**[[Media:RegXForm_RegUC-001.tfm.txt|result transform file (ITK .tfm file, load into slicer and apply to the target volume)]]
**Tutorials (step-by -step walk through):
***[[Media:RegLib_C01_PPTTutorial_TumorGrowth.ppt.zip‎|download power point tutorial (zip file, 2.8 MB, filename: RegLib_C01_PPTTutorial_TumorGrowth.ppt.zip) ]]
**[[Media:RegLib_C01_TumorGrowth_MultiresSolution_Dec09.zip‎|Multiresolution testresult package (Data,Xform, Solution, zip file 16.5 MB) ]]
**[http://www.insight-journal.org/midas/item/bitstream/2332 Download package from MIDAS server (Data,Xform) ]

[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]



=== Discussion: Registration Challenges ===
*accuracy is the critical criterion here. We need the registration error (residual misalignment) to be smaller than the change we want to measure/detect. Agreement on what constitutes good alignment can therefore vary greatly.
*the two images have strong differences in coil inhomogeneity. This affects less the registration quality but hampers evaluation. Most of the difference does not become apparent until after registration in direct juxtaposition. Bias field correction beforehand is recommended.
*we have slightly different voxel sizes
*if the pathology change is substantial it might affect the registration.

=== Discussion: Key Strategies ===
*the two images have identical contrast, hence we consider "sharper" cost functions, such as NormCorr or MeanSqrd
*general practice is to register the follow-up to the baseline. However here the follow-up has slightly higher resolution. From an image quality/data perspective it would be better to use the highest resolution image as your fixed/reference. But here follow the most common convention, i.e. fixed image is the baseline.
*because we seek to assess/quantify regional size change, we must use a rigid (6DOF) scheme, i.e. we must exclude scaling.
*if the pathology change is soo large that it might affect the registration, we should mask it out. The simplest way to do this is to build a box ROI from the ROItool and feed it as input to the registration. Remember that masking does not mean that masked areas aren't matched, they just do not contribute to the cost function driving the registration, but move along passively. Next more involved level would be to outline the tumor. If a segmentation is available, you can use that.
*these two images are not too far apart initially, so we reduce the default of expected translational misalignment
*because accuracy is more important than speed here, we increase the sampling rate from the default 2% to 15%.
*we also expect minimal differences in scale & distortion: so we can either set the expected values to 0 or run a rigid registration
*we test the result in areas with good anatomical detail and contrast, far away from the pathology. With rigid body motion a local measure of registration accuracy is representative and can give us a valid limit of detectable change.

@@ Line 70: / Line 70: @@
 |-
 |nonrigid registered (7x7x7 BSpline unmasked)
-|nonrigid registered (7x7x7 BSpline masked)
+|nonrigid registered (7x7x7 BSpline '''masked''')
 |}

@@ Line 43: / Line 43: @@
 ###select a new transform "Linear Transform", rename to "Xf1_affine"
 ##Leave all other settings at default
-*'''Phase I:  Register BSpline'''
+*'''Phase II:  [optional]: generate skull mask
-###select a new volume "Output Image Volume'', rename to "DTI_base_Xf1"
+#open ''Skull Stripper for Structural MRI'' Module (Extension module)
 ##Registration Parameters: increase ''Number Of Samples'' to 200,000
 ##Registration Parameters: set  ''Number Of Grid Subdivisions'' to 7x7x7
 ##Leave all other settings at default
 === Registration Results===

@@ Line 32: / Line 32: @@
 {| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C37_unreg.png|400px|center|unregistered]]
 |-
 |[[Image:RegLib_C37_Xf1.gif|400px|center|rigid]]
 |[[Image:RegLib_C37_Xf2.gif|400px|center|affine]]
 |-
 |[[Image:RegLib_C37_Xf3.gif|400px|center|BSpline (7x7x7) unmasked]]
 |[[Image:RegLib_C37_Xf4.gif|400px|center|BSpline (7x7x7) masked]]
 |-
 |nonrigid registered (7x7x7 BSpline unmasked)
@@ Line 50: / Line 49: @@
 ===Download ===
 *Data
-**[[Media:RegLib_C37_Data.zip‎ ‎|'''RegLib_C37_Data''' , image data, resets & solution transforms  <small> (NRRD files, zip file xx MB) </small>]]'''
+**[[Media:RegLib_C37_Data.zip‎ ‎|'''RegLib_C37_Data''' , image data, resets & solution transforms  <small> (NRRD files, zip file 41 MB) </small>]]'''
 *Presets
 **[[Media:RegLib_C37_Presets.mrml‎|'''RegLib_C37_Presets''' Presets for BRAINSFIT registration <small> (.mrml file 12 kB) </small>]]'''

@@ Line 40: / Line 40: @@
 |-
 |original unregistered
 |rigid registered
 |affine registered
 |nonrigid registered (7x7x7 BSpline unmasked)
 |nonrigid registered (7x7x7 BSpline masked)

@@ Line 6: / Line 6: @@
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C37_Thumb1.png|200px|lleft|this is the fixed reference image. All images are aligned into this space]]
+|[[Image:RegLib_C37_Thumb1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
-|[[Image:RegArrow_Nonrigid.png|100px|lleft]]
+|[[Image:RegArrow_NonRigid.png|100px|lleft]]
-|[[Image:RegLib_C37_Thumb2.png|200px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
+|[[Image:RegLib_C37_Thumb2.png|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
 |-
 |fixed image/target
@@ Line 31: / Line 31: @@
 === Registration Results===
 {| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C37_unreg.gif|400px|center|unregistered]]
+|[[Image:RegLib_C37_unreg.png|400px|center|unregistered]]
 |[[Image:RegLib_C37_Xf1.gif|400px|center|rigid]]
 |[[Image:RegLib_C37_Xf2.gif|400px|center|affine]]
 |[[Image:RegLib_C37_Xf3.gif|400px|center|BSpline (7x7x7) unmasked]]
 |[[Image:RegLib_C37_Xf4.gif|400px|center|BSpline (7x7x7) masked]]
@@ Line 45: / Line 47: @@
 ===Download ===
-*Data:
+*Data
-**'''[[Media:RegLib_C37_Data.zip‎|Image Data + solutions package  <small> (Data, Solution, zip file qqMB) </small>]]'''
+**[[Media:RegLib_C37_Data.zip‎ ‎|'''RegLib_C37_Data''' , image data, resets & solution transforms  <small> (NRRD files, zip file xx MB) </small>]]'''
-*Presets:
+*Presets
-[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
+**[[Media:RegLib_C37_Presets.mrml‎|'''RegLib_C37_Presets''' Presets for BRAINSFIT registration <small> (.mrml file 12 kB) </small>]]'''
-*Documentation
+**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
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 comment
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@@ Line 17: / Line 17: @@
 === Modules ===
 '''Slicer 3.6.1''' recommended modules:
-*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]
+*[https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit]
-*[http://www.slicer.org/slicerWiki/index.php/Modules:SkullStripperModule Skull-Stripper Module]
+*[https://www.slicer.org/wiki/Modules:SkullStripperModule Skull-Stripper Module]
 ===Objective / Background ===

@@ Line 28: / Line 28: @@
 *reference/fixed : T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal
 *moving: T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal
 === Registration Results===