I am trying to fix the freesurfer results after running recon-all with fmriprep. The problem is in the pial surface, wm, and brain masks because of some inhomogeneity in the 7T MPRAGE data. I am fixing the brain mask following the instructions here:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview . After I fix the brain mask, I am trying to run the code for surfaces to be updated based on the updated brain mask with "recon-all -autorecon-pial" command. Every time I tried
with different subjects, it updated the surfaces but not in a corrected way. The results for surfaces never really changed, and the mri/brain.mgz file was never even updated. One solution is to run recon-all -all with the options I want for skullstripping
but it is time consuming for me and I usually prefer the fmriprep's pipeline for freesurfer. Can you help me find a way to fix this without having to rerun all the analysis?
You can find an example log file where you can see the skullstripping with different settings starting on Line 3959 and the calling of autorecon-pial starting on Line 4245.