Difference between revisions of "Projects:RegistrationLibrary:RegLib C04"
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[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <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 04: <br> Intra-subject Brain MR of Multiple Sclerosis: Multi-contrast series for lesion change assessment = | + | = <small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png|150px]] Slicer Registration Library Case 04: <br> Intra-subject Brain MR of Multiple Sclerosis: Multi-contrast series for lesion change assessment = |
=== Input === | === Input === | ||
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | ||
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|[[Image:Reglib_C04_Thumb_Gd1.jpg|150px|lleft|this is the intra-subject moving image. ]] | |[[Image:Reglib_C04_Thumb_Gd1.jpg|150px|lleft|this is the intra-subject moving image. ]] | ||
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| − | |[[Image: | + | |exam 1 PD |
| + | |exam 1 T2 | ||
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| + | |exam 1 T1-Gd | ||
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| + | |[[Image:RegArrow_AffineVert.png|100px|lleft]] | ||
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|[[Image:RegArrow_Affine.png|100px|lleft]] | |[[Image:RegArrow_Affine.png|100px|lleft]] | ||
|[[Image:Reglib_C04_Thumb_Gd2.jpg|150px|lleft|this is the moving image. ]] | |[[Image:Reglib_C04_Thumb_Gd2.jpg|150px|lleft|this is the moving image. ]] | ||
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| + | |exam 2 PD | ||
| + | |exam 2 T2 | ||
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| + | |exam 2 T1-Gd | ||
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=== Modules === | === 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:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]''' | *'''Slicer 3.6.1 recommended modules: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]''' | ||
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===Objective / Background === | ===Objective / Background === | ||
Revision as of 13:46, 13 September 2010
Home < Projects:RegistrationLibrary:RegLib C04Back to ARRA main page
Back to Registration main page
Back to Registration Use-case Inventory
v3.6.1 
Slicer Registration Library Case 04:
Intra-subject Brain MR of Multiple Sclerosis: Multi-contrast series for lesion change assessment
Input
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| exam 1 PD | exam 1 T2 | exam 1 T1-Gd | |
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| exam 2 PD | exam 2 T2 | exam 2 T1-Gd |
Modules
- Slicer 3.6.1 recommended modules: BrainsFit, Robust Multiresolution Affine
Objective / Background
This scenario occurs in many forms whenever we wish to assess change in a series of multi-contrast MRI. The follow-up scan(s) are to be aligned with the baseline, but also the different series within each exam need to be co-registered, since the subject may have moved between acquisitions. Hence we have a set of nested registrations. This particular exam features a dual echo scan (PD/T2), where the two structural scans are aligned by default. The post-contrast T1-GdDTPA scan however is not necessarily aligned with the dual echo. Also the post-contrast scan is taken with a clipped field of view (FOV) and a lower axial resolution, with 4mm slices and a 1mm gap (which we treat here as a de facto 5mm slice).
Keywords
MRI, brain, head, intra-subject, multiple sclerosis, MS, multi-contrast, change assessment, dual echo, nested registration
Input Data
reference/fixed : PD baseline exam , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation.- reference/fixed : T2 baseline exam , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation.
moving: T1-GdDTPA baseline exam 0.9375 x 0.9375 x 5 mm voxel size, axial acquisition.- moving: PD follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition.
tag: T2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition.- moving:T1-GdDTPA follow-up exam0.9375 x 0.9375 x 5 mm voxel size, axial acquisition.
Registration Challenges
- we have multiple nested transforms: each exam is co-registered within itself, and then the exams are aligned to eachother
- potential pathology change can affect the registration
- anisotropic voxel size causes difficulty in rotational alignment
- clipped FOV and low tissue contrast of the post-contrast scan
Key Strategies
- we first register the post-contrast scans within each exam to the PD
- we also move the T2 exam within the same Xform
- second we register the follow-up PD scan to the baseline PD
- we then nest the first alignment within the second
- we compare T1Gd to T1Gd, which went through 2 transforms. We correct residual misalignment with a 3rd correction transform
- because of the contrast differences and anisotropic resolution we use Mutual Information as cost function for better robustness
- we adjust the expected translation and rotational parameter settings to the visual assessment of the input data (i.e. initial misalignment)
Registration Results
Download
- Registration Library Case 04: MS Multi-contrast series (PD,T2, T1-GdDTPA): Lesion change assessment (Data,Presets, Solution, zip file 17 MB)
- download/view guided video tutorial
- download power point tutorial
Link to User Guide: How to Load/Save Registration Parameter Presets
