Hi Bruce,
Thank you for your reply. I've uploaded the .mgz and surfaces using FTP to FreeSurfer. Why is it that it may not be possible to get good surfaces with extensive strokes?
Thank you, Sabrina ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Thursday, May 19, 2016 11:24:51 AM To: Freesurfer support list Subject: Re: [Freesurfer] Brainmask edit error
Hi Sabrina
it's tough to tell from just the 2 slices. If you upload the subject one of us will take a look, but it may not be possible to get good surfaces with that extensive a stroke
cheers Bruce On Wed, 18 May 2016, Sabrina Yu wrote:
Hello,
I'm having problems with regenerating the surfaces for stroke cases after editing the brainmask.mgz file. In the aseg.mgz file, the brain matter around lesion area is correctly classified as brain matter. In the pial surface, this brain matter is not included.
I've tried to edit the brainmask.mgz file to include this region, but when I run: recon-all -subjid <SUBJECT> -autorecon2-pial, the surfaces generated are not changed at all.
I have attached some images to this email. I'm new to Freesurfer, so any help would be greatly appreciated.
Thank you.