Difference between revisions of "Projects:RegistrationLibrary:RegLib C31"
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− | == | + | [[Projects:ARRASuplements|Back to ARRA main page]] <br> |
+ | [[Projects:RegistrationDocumentation|Back to Registration main page]] <br> | ||
+ | [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br> | ||
+ | |||
+ | = <small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png|150px]] Slicer Registration Library Case xx: TBI = | ||
+ | === Input === | ||
+ | |||
+ | === 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:RegisterImages-Documentation-3.6 Expert Automated Registration] | ||
+ | |||
+ | ===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=== | ||
+ | *reference/fixed : T1.1 baseline exam of acute TBI , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation. | ||
+ | *fixed T2.1 baseline exam , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation. -> (aligned with PD.1, not used for registering) | ||
+ | *moving: T1.1 (GdDTPA contrast-enhanced scan) baseline exam 0.9375 x 0.9375 x 5 mm voxel size, axial acquisition. | ||
+ | *moving: PD.2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition. | ||
+ | *moving: T2.2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition. -> same orientation as PD2, will have same transform applied | ||
+ | *moving:T1.2-GdDTPA follow-up exam0.9375 x 0.9375 x 5 mm voxel size, axial acquisition. -> undergoes 2 transforms: first to PD.2, then to PD.1 | ||
+ | |||
+ | ===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''' | ||
+ | #Load T1 MPRAGE datasets via Load Volume... | ||
+ | #volumes are note well centered, i.e. their physical origin defined in the image header differs; we therefore first center both images: | ||
+ | ##Go to ''Volumes'' module, open ''Info'' tab | ||
+ | ##From ''Active Volume'' menu, select each image in turn, then click the ''Center Image'' button | ||
+ | *'''Align Exam 1: FLAIR''' 1st pass: unmasked | ||
+ | #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: e1_T1, moving image: e1_FLAIR | ||
+ | ##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'' | ||
+ | ##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 | ||
+ | ##Go back to the ''Data'' module: you should see the e1_FLAIR image moved under the newly created transform | ||
+ | ##Select "E1_T1" as background and ''e1_FLAIR'' 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 | ||
+ | *'''Align Exam 1: FLAIR''' 2nd pass: masked | ||
+ | #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 | ||
+ | ##To set all parameters from presets, from the ''ParameterSet'' menu, select "Xf1c_e1_FLAIR-T1_masked", else choose settings below: | ||
+ | ##Fixed Image: e1_T1, moving image: e1_FLAIR | ||
+ | ##Registration Phases: select ''Include Rigid'', "IncludeScaleVersor3D" and ''Include Affine''. Make sure ''no'' initialization phases are selected. | ||
+ | ##Output Settings: under SlicerLinear Transform, select "Create New Linear Transform'', then select ''Rename" and rename it to ''Xf1c_e1_FLAIR-T1_masked'' | ||
+ | ##Registration Parameters: increase the ''Number of Samples'' field to 200,000 | ||
+ | ##Control of Mask Processing tab: check "ROI" box, | ||
+ | ###Input Fixed Mask, select "e1_ICC", | ||
+ | ###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=== | ||
+ | [[Image:RegLib_C18_AGif_e1.gif|300px|Exam 1 co-registered]] Exam 1 co-registered: FLAIR and T2 aligned with T1 <br><br> | ||
+ | [[Image:RegLib_C18_AGif_e2.gif|300px|Exam 2 co-registered]] Exam 1 co-registered: FLAIR and T2 aligned with T1 <br><br> | ||
+ | [[Image:RegLib_C18_AGif_e2-e1.gif|300px|Exam 2 aligned to Exam 1]] Exam 2 aligned to Exam 1 (showing FLAIR and T2 of exam 2 also) <br> |
Revision as of 14:33, 3 November 2010
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Contents
v3.6.1 Slicer Registration Library Case xx: TBI
Input
Modules
- Slicer 3.6.1 recommended modules: BrainsFit, Expert Automated Registration
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
- reference/fixed : T1.1 baseline exam of acute TBI , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation.
- fixed T2.1 baseline exam , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation. -> (aligned with PD.1, not used for registering)
- moving: T1.1 (GdDTPA contrast-enhanced scan) baseline exam 0.9375 x 0.9375 x 5 mm voxel size, axial acquisition.
- moving: PD.2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition.
- moving: T2.2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition. -> same orientation as PD2, will have same transform applied
- moving:T1.2-GdDTPA follow-up exam0.9375 x 0.9375 x 5 mm voxel size, axial acquisition. -> undergoes 2 transforms: first to PD.2, then to PD.1
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
- Load T1 MPRAGE datasets via Load Volume...
- volumes are note well centered, i.e. their physical origin defined in the image header differs; we therefore first center both images:
- Go to Volumes module, open Info tab
- From Active Volume menu, select each image in turn, then click the Center Image button
- Align Exam 1: FLAIR 1st pass: unmasked
- 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: e1_T1, moving image: e1_FLAIR
- 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
- 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
- Go back to the Data module: you should see the e1_FLAIR image moved under the newly created transform
- Select "E1_T1" as background and e1_FLAIR 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
- Align Exam 1: FLAIR 2nd pass: masked
- 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
- To set all parameters from presets, from the ParameterSet menu, select "Xf1c_e1_FLAIR-T1_masked", else choose settings below:
- Fixed Image: e1_T1, moving image: e1_FLAIR
- Registration Phases: select Include Rigid, "IncludeScaleVersor3D" and Include Affine. Make sure no initialization phases are selected.
- Output Settings: under SlicerLinear Transform, select "Create New Linear Transform, then select Rename" and rename it to Xf1c_e1_FLAIR-T1_masked
- Registration Parameters: increase the Number of Samples field to 200,000
- Control of Mask Processing tab: check "ROI" box,
- Input Fixed Mask, select "e1_ICC",
- 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
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
Exam 1 co-registered: FLAIR and T2 aligned with T1
Exam 1 co-registered: FLAIR and T2 aligned with T1
Exam 2 aligned to Exam 1 (showing FLAIR and T2 of exam 2 also)