The basic steps in the FSL FIRST shape analysis are as follows:
- Start with T1 images
- Manually aligning the T1 with MNI space sometimes improves segmentation.
- Segment using run_first_all (creates "bvars") files
- Convert to nifti format, include mean structure surface saved as mask, and 4D file with vertex distances from mean (for each subject, in voxels)
- Run stats on distance file
- Visualize and quantify
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