Overview

The basic steps in the FSL FIRST shape analysis are as follows:

1. Start with T1 images
   • Manually aligning the T1 with MNI space sometimes improves segmentation.
2. Segment using run_first_all (creates "bvars") files
3. Convert to nifti format, include mean structure surface saved as mask, and 4D file with vertex distances from mean (for each subject, in voxels)
4. Run stats on distance file
5. Visualize and quantify