Difference between revisions of "Projects:RegistrationLibrary:RegLib C04"
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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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| − | |exam 1 PD | + | |exam 1: PD |
| − | |exam 1 T2 | + | |exam 1: T2 |
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| − | |exam 1 T1-Gd | + | |exam 1: T1-Gd |
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|[[Image:RegArrow_AffineVert.png|100px|lleft]] | |[[Image:RegArrow_AffineVert.png|100px|lleft]] | ||
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|[[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. ]] | ||
|- | |- | ||
| − | |exam 2 PD | + | |exam 2: PD |
| − | |exam 2 T2 | + | |exam 2: T2 |
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| − | |exam 2 T1-Gd | + | |exam 2: T1-Gd |
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===Input Data=== | ===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=== | ===Registration Challenges=== | ||
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===Key Strategies=== | ===Key Strategies=== | ||
*we first register the post-contrast scans within each exam to the PD | *we first register the post-contrast scans within each exam to the PD | ||
| + | *second we register the follow-up PD scan to the baseline PD | ||
*we also move the T2 exam within the same Xform | *we also move the T2 exam within the same Xform | ||
| − | |||
*we then nest the first alignment within the second | *we then nest the first alignment within the second | ||
| − | |||
*because of the contrast differences and anisotropic resolution we use Mutual Information as cost function for better robustness | *because of the contrast differences and anisotropic resolution we use Mutual Information as cost function for better robustness | ||
| − | |||
=== Registration Results=== | === Registration Results=== | ||
Revision as of 13:49, 13 September 2010
Home < Projects:RegistrationLibrary:RegLib C04Back to ARRA main page
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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
- second we register the follow-up PD scan to the baseline PD
- we also move the T2 exam within the same Xform
- we then nest the first alignment within the second
- because of the contrast differences and anisotropic resolution we use Mutual Information as cost function for better robustness
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
