Difference between revisions of "Projects:RegistrationLibrary:RegLib C31"

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*'''Align Exam 2 to Exam 1: T1''' 1st pass: unmasked
 
*'''Align Exam 2 to Exam 1: T1''' 1st pass: unmasked
 
#Open ''Registration / BRAINSFit'' module
 
#Open ''Registration / BRAINSFit'' module
−
##To set all parameters from presets, from the ''ParameterSet'' menu, select "Xf1_e1_FLAIR-T1_unmasked", else choose settings below:
+
##Fixed Image: T1_e1, moving image: T1_e2
−
##Fixed Image: e1_T1, moving image: e1_FLAIR
 
 
##Registration Phases: select "Initialize with CenterOfHeadAlign",  ''Include Rigid'', "IncludeScaleVersor3D" and ''Include Affine''
 
##Registration Phases: select "Initialize with CenterOfHeadAlign",  ''Include Rigid'', "IncludeScaleVersor3D" and ''Include Affine''
−
##Output Settings: under SlicerLinear Transform, select "Create New Linear Transform'', then select ''Rename" and rename it to ''Xf1_e1_FLAIR-T1''
+
##Output Settings: under SlicerLinear Transform, select "Create New Linear Transform'', then select ''Rename" and rename it to ''Xf1_e2-e1_Affine''
 
##Registration Parameters: increase the ''Number of Samples'' field to 200,000
 
##Registration Parameters: increase the ''Number of Samples'' field to 200,000
 
##Leave all other settings at defaults & Click:  ''Apply''. Registration should complete within ~ 30 seconds
 
##Leave all other settings at defaults & Click:  ''Apply''. Registration should complete within ~ 30 seconds
−
##Go back to the ''Data'' module: you should see the e1_FLAIR image moved under the newly created transform
+
##Go back to the ''Data'' module: you should see the T1_e2 image moved under the newly created transform
−
##Select "E1_T1" as background and ''e1_FLAIR'' as new foreground, toggle to see alignment
+
##Select "T1_e1" as background and ''T2_e2'' as new foreground, toggle to see alignment
−
##you will notice a small but distinct residual translational misalignment, apparent on axial and sagittal slices. This likely arises from dominant edges of the skull. We rerun a 2nd pass with masks
+
##due to the strong deformations an affine alignment alone does not achieve a perfect match. We can extend the DOF to non-rigid BSpline transforms, but must be aware that doing so might remove differences of interest:
−
*'''Align Exam 1: FLAIR''' 2nd pass: masked
+
*'''Align Exam 2:''' 2nd pass: nonrigid
−
#we obtain a mask for the moving image (e1_FLAIR) by sending the mask for the fixed image (e1_ICC) through the inverse of the above transform
 
−
##From File menu, select ''Add Data'' & reload a second copy of the above transform  ''Xf1_e1_FLAIR-T1'' and the labelmap "e1_ICC.nrrd"
 
−
##rename Xform to " ''Xf1i_e1_T1-FLAIR'' and the mask to "e1_FLAIR_mask"
 
−
##go to the ''Transforms'' module, select the ''Xf1i_e1_T1-FLAIR'' transform and then click on the ''Invert'' button
 
−
##go to the ''Data'' module and drag the node for "e1_FLAIR_mask" inside the transform node ''Xf1i_e1_T1-FLAIR''
 
−
##right click on the ''Xf1i_e1_T1-FLAIR'' node and select ''Harden Transform''. We now have an approximate mask for the moving FLAIR image.
 
 
#Open ''Registration / BRAINSFit'' module
 
#Open ''Registration / BRAINSFit'' module
−
##To set all parameters from presets, from the ''ParameterSet'' menu, select "Xf1c_e1_FLAIR-T1_masked", else choose settings below:
+
##Fixed Image: T1_e1, moving image: T1_e2
−
##Fixed Image: e1_T1, moving image: e1_FLAIR
+
##From "Initialize with previously generated transform" & select the above affine ''Xf1_e2-e1_Affine''
−
##Registration Phases: select ''Include Rigid'', "IncludeScaleVersor3D" and ''Include Affine''. Make sure ''no'' initialization phases are selected.
+
##Registration Phases: select only ''Include BSpline''.  
−
##Output Settings: under SlicerLinear Transform, select "Create New Linear Transform'', then select ''Rename" and rename it to ''Xf1c_e1_FLAIR-T1_masked''
+
##Output Settings: under SlicerBSpline Transform, select "Create New BSpline Transform'', then select ''Rename" and rename it to ''Xf2_e2-e1_BSpl''
 
##Registration Parameters: increase the ''Number of Samples'' field to 200,000
 
##Registration Parameters: increase the ''Number of Samples'' field to 200,000
−
##Control of Mask Processing tab: check "ROI" box,
+
##Leave all other settings at defaults & Click:  ''Apply''. Registration should complete within 3 minutes.
−
###Input Fixed Mask, select "e1_ICC", 
+
##You should see the earlier residual misalignment reduced, but strong distortions applied to the e2 image (see results below)
−
###Input Moving Mask, select "e1_FLAIR_mask"
 
−
##Leave all other settings at defaults & Click:  ''Apply''. Registration should complete within ~ 40 seconds
 
−
##You should see the earlier residual misalignment mostly gone.
 
−
*'''Align Exam 1: T2'''
 
−
#The T2 image is not far in pose from the T1 and also does not have the same skull-contrast issue as the FLAIR, we register directly to the T1 w/o masking
 
−
#Open ''Registration / BRAINSFit'' module
 
−
##To set all parameters from presets, from the ''ParameterSet'' menu, select "Xf2_e1_T2-T1_unmasked", else choose settings below:
 
−
##Fixed Image: e1_T1, moving image: e1_T2
 
−
##Registration Phases: select ''Include Rigid'', "IncludeScaleVersor3D" and ''Include Affine''.
 
−
##Output Settings: under SlicerLinear Transform, select "Create New Linear Transform'', then select ''Rename" and rename it to ''Xf2_e1_T2-T1''
 
−
##Registration Parameters: increase the ''Number of Samples'' field to 200,000
 
−
##Leave all other settings at defaults & Click:  ''Apply''. Registration should complete within ~ 30 seconds
 
−
*'''Align Exam 2:'''
 
−
**repeat the above steps for exam 2, i.e. align e2_FLAIR and e2_T2 with e2_T1
 
−
**the above issue with the FLAIR-T1 residual does not arise for the follow-up exam, hence direct registration (unmasked) is possible
 
−
**Registration presets: BRAINSFit see Xf3_ and Xf4_ for FLAIR and T2, respectively
 
−
[[Image:RegLib_C18_RegHierarchy.png|200px|right| the MRML node tree shows the hierarchy of multiple transfoms]] the MRML node tree shows the hierarchy of multiple transfoms.
 
−
*'''Align Exam 2-1:'''
 
−
#finally we align the T1 references of exam 1 and 2, i.e. we align e2_T1 with e1_T1:
 
−
#Registration presets: BRAINSFit see Xf5_
 
−
#parameters: defaults except increase sample rate to 200,000.
 
−
#here we have genuine masks for both images: ''Control of Mask Processing Tab'':
 
−
##Control of Mask Processing tab: check "ROI" box,
 
−
##Input Fixed Mask, select "e1_ICC", 
 
−
##Input Moving Mask, select "e2_ICC"
 
−
##Leave all other settings at defaults & Click:  ''Apply''. Registration should complete within ~ 20 seconds
 
−
*'''Combine Transforms:'''
 
−
#to align all images in a common space, we combine a hierarchy of transforms, i.e. the e2_FLAIR undergoes both the Xf3_e2_FLAIR-T1 and the Xf4_e2-e1: See image on the right for what the final hierarchy should look like.
 
−
#right-click on the nested transforms and select ''Harden Transforms'' from the pulldown menu.  Rename the hardened transforms to indicate the direct alignment with e1_T1.
 
−
*''Resample''
 
−
#resample all images with their respective transforms, using the ''Filtering ->  Resample Scalar/Vector/DWI Volume'' module.
 
−
#within the module, select "ws" as interpolation type
 
−
*''Nonrigid extension''
 
−
#there is some residual distortion in the alignment of e2_T1 to e1_T1. Optionally one can address this via another separate nonrigid BSpline registration. However combining the Affine with the BSpline is not straightforward (as of v.3.6.1), to do this follow this outline:
 
−
##resample e2_T1 according to Xf5 : e2_T1_Xf5
 
−
##Perform a BSpline ''only'' alignment : Xf6_e2-e1_BSpline that aligns e2_T1_Xf5 with e1_T1. Grid size 3-5.
 
−
##Save resulting Xform
 
−
##Open Xform file and other saved affine transforms in Text Editor
 
−
##Paste the affine portion at the bottom of the BSpline and save under new name.
 
  
 
=== Registration Results===
 
=== Registration Results===

Revision as of 16:10, 3 November 2010

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v3.6.1 Slicer3-6Announcement-v1.png Slicer Registration Library Case xx: TBI

Input

Modules

Objective / Background

We seek to align two exams (acute baseline and follow-up) as well as all series within exams into a common space for direct evaluation of regional change.

Input Data

  • inter-exam
    • reference/fixed : T1_e1 baseline exam of acute TBI , 512 x 512 x 160 ; 0.5 x 0.5 x 1 mm voxel size, axial acquisition, RAS orientation.
    • moving:T1_e2 follow-up exam of acute TBI , 512 x 512 x 160 ; 0.5 x 0.5 x 1 mm voxel size, axial acquisition, RAS orientation.
  • intra-exam

Registration Challenges

  • we have multiple nested transforms: each exam is co-registered within itself, and then the exams are aligned to eachother
  • strong pathology (hemorrhage?) present at different amounts in the two exams

Key Strategies

  • we first register the scans within each exam to the T1
  • second we register the follow-up T1 scan to the baseline T1
  • we then nest the first alignment within the second

Procedure

  • Load & Center
  1. Load T1 MPRAGE datasets via Load Volume...
  2. volumes are note well centered, i.e. their physical origin defined in the image header differs; we therefore first center both images:
    1. Go to Volumes module, open Info tab
    2. From Active Volume menu, select each image in turn, then click the Center Image button
    3. note how Image origin changes for T1_e1 from 121,-97,-97 to 128,-128,-80 and for T1_e2 from 129,-106,-66 to 128,-128,-80
    4. now that both images have same center their initial misalignment can be seen by placing T1_e1 in the background and T1_e in the foreground and using the toggle-switch
  • Align Exam 2 to Exam 1: T1 1st pass: unmasked
  1. Open Registration / BRAINSFit module
    1. Fixed Image: T1_e1, moving image: T1_e2
    2. Registration Phases: select "Initialize with CenterOfHeadAlign", Include Rigid, "IncludeScaleVersor3D" and Include Affine
    3. Output Settings: under SlicerLinear Transform, select "Create New Linear Transform, then select Rename" and rename it to Xf1_e2-e1_Affine
    4. Registration Parameters: increase the Number of Samples field to 200,000
    5. Leave all other settings at defaults & Click: Apply. Registration should complete within ~ 30 seconds
    6. Go back to the Data module: you should see the T1_e2 image moved under the newly created transform
    7. Select "T1_e1" as background and T2_e2 as new foreground, toggle to see alignment
    8. due to the strong deformations an affine alignment alone does not achieve a perfect match. We can extend the DOF to non-rigid BSpline transforms, but must be aware that doing so might remove differences of interest:
  • Align Exam 2: 2nd pass: nonrigid
  1. Open Registration / BRAINSFit module
    1. Fixed Image: T1_e1, moving image: T1_e2
    2. From "Initialize with previously generated transform" & select the above affine Xf1_e2-e1_Affine
    3. Registration Phases: select only Include BSpline.
    4. Output Settings: under SlicerBSpline Transform, select "Create New BSpline Transform, then select Rename" and rename it to Xf2_e2-e1_BSpl
    5. Registration Parameters: increase the Number of Samples field to 200,000
    6. Leave all other settings at defaults & Click: Apply. Registration should complete within 3 minutes.
    7. You should see the earlier residual misalignment reduced, but strong distortions applied to the e2 image (see results below)

Registration Results

Exam 1 co-registered unregistered exam 1 & 2
Exam 2 co-registered Exam 2 aligned to Exam 1 (affine only)
Exam 2 aligned to Exam 1 Exam 2 aligned to Exam 1 (affine+BSpline)
Exam 2 aligned to Exam 1 BSpline deformation only of Exam 2

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