Hey Freesurfers, I've been trying to register my FEAT data to my Freesurfer data via reg-feat2anat in order to get V1 binary masks:

reg-feat2anat --->aparc/aseg2feat --->fslmaths.

It seemed to work ok, and I extracted time series for my areas of interest and ran a PPI analysis in FSL. When reviewing my results I discovered that for two people their brains were flipped 90 degrees around multiple axes compared with the group. So I decided to go back to reg-feat2anat and manually edit the registration of all my subjects. For most people the edits were extremely minor. For the 2 highly problematic ones, appropriate rotations were made.

When I returned to my PPI analysis, I found that now all of my brains are rotated by at least 45 degrees sometimes about multiple axes. I am thoroughly perplexed.

Does anyone know what might have gone wrong?

Thanks. Michelle