Hi Batool
if you need to change the watershed you will need to rerun everything from there forward. All of autorecon2 and autorecon3 I think at least
cheers Bruce
On Wed, 14 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
We have a subject on which we had to do adjust the watershed parameters for, since there was some brain missing from the brainmask.mgz. The watershed itself worked, but after that, we needed to regenerate the surfaces after the bad skull strip was fixed, and we ran "recon-all -autorecon-pial -subjid <subject name>"
That seemed to not work though, and it still shows that the surfaces do not include the new brain matter. Attached is an image of the output. Is there anything else we can try to regenerate these surfaces correctly?
Thank you!
Batool