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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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. > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
