FSL describes To prepare for the shape analysis as "Vertex Analysis," which is a section in the User Guide. There is a simple preparation step, and then there is running the model, which is a single step but with several options. , there are a couple of preparation steps: combining the individual segmented structures into one file, and creating a design matrix to indicate which file belongs to which group. The segmentations can also be checked at this point.
Combining individual files: concat_bvars
...