Projects:RegistrationLibrary:RegLib C10
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Slicer Registration Library Exampe #10: Co-registration of probabilistic tissue atlas for subsequent EM segmentation
Objective / Background
This is an example of sparse atlas co-registration. Not all atlases have an associated reference image that can be used for registration. Because the atlas represents a map of a particular tissue class probability, its contrast differs significantly from the target image.
Keywords
MRI, brain, head, inter-subject, probabilistic atlas, atlas-based segmentation
Input Data
- reference/fixed : T1w axial, 1mm resolution in plane, 3mm slices
- moving: Probabilistic Tissue atlas,
x 36 x 9
Registration Results
Download
- download entire package (Data,Tutorial, Solution, zip file xx MB)
- Presets
- Tutorial only
- Image Data only
Discussion: Registration Challenges
- Because the atlas represents a map of a particular tissue class probability, its contrast differs significantly from the target image.
- The two images may have strong differences in voxel sizes and voxel anisotropy. If the orientation of the highest resolution is not the same in both images, finding a good match can be difficult.
- The two images represent different anatomies, a non-rigid registration is required
Discussion: Key Strategies
- Because of the strong differences in image contrast, Mutual Information is recommended as the most robust metric.
- masking (skull stripping) is highly recommended to obtain good results.
- because speed is not that critical, we increase the sampling rate from the default 2% to 15%.
- we also expect larger differences in scale & distortion than with regular structural scans: so we significantly (2x-3x) increase the expected values for scale and skew from the defaults.
- a good affine alignment is important before proceeding to non-rigid alignment to further correct for distortions.