Hey Freesurfers,<br>I&#39;ve been trying to register my FEAT data to my Freesurfer data via reg-feat2anat in order to get V1 binary masks:<br><br>reg-feat2anat ---&gt;aparc/aseg2feat ---&gt;fslmaths. <br><br> 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.<br>
<br>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.<br><br>Does anyone know what might have gone wrong?    <br>
<br>Thanks.<br>Michelle<br>