Difference between revisions of "Projects:RegistrationLibrary:RegLib C04"
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|[[Image:Button_green_moving.jpg|40px|lleft]] PD axial | |[[Image:Button_green_moving.jpg|40px|lleft]] PD axial | ||
|[[Image:Button_blue_tag.jpg|40px|lleft]] T2 axial | |[[Image:Button_blue_tag.jpg|40px|lleft]] T2 axial | ||
− | |[[Image: | + | |[[Image:Button_green_moving.jpg|40px|lleft]] T1-GdDTPA |
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|0.9375 x 0.9375 x 3 mm axial<br> 256 x 256 x 51<br>RAS | |0.9375 x 0.9375 x 3 mm axial<br> 256 x 256 x 51<br>RAS | ||
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*[[Image:Button_green_moving_white.jpg|20px]] moving: T1-GdDTPA baseline exam 0.9375 x 0.9375 x 5 mm voxel size, axial acquisition. | *[[Image:Button_green_moving_white.jpg|20px]] moving: T1-GdDTPA baseline exam 0.9375 x 0.9375 x 5 mm voxel size, axial acquisition. | ||
*[[Image:Button_green_moving_white.jpg|20px]] moving: PD follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition. | *[[Image:Button_green_moving_white.jpg|20px]] moving: PD follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition. | ||
− | *[[Image:Button_blue_tag_white.jpg|20px]]tag: T2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition. | + | *[[Image:Button_blue_tag_white.jpg|20px]] tag: T2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition. |
*[[Image:Button_green_moving_white.jpg|20px]] moving:T1-GdDTPA follow-up exam0.9375 x 0.9375 x 5 mm voxel size, axial acquisition. | *[[Image:Button_green_moving_white.jpg|20px]] moving:T1-GdDTPA follow-up exam0.9375 x 0.9375 x 5 mm voxel size, axial acquisition. | ||
Revision as of 21:56, 19 February 2010
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Contents
Slicer Registration Library Case 04: Intra-subject Brain MR of Multiple Sclerosis: Multi-contrast series for lesion change assessment
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
Registration Result: FLAIR + segmentation aligned with SPGR
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