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
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