because it violates too many of our assumptions about the topology and geometry of the brain.
cheers Bruce On Mon, 23 May 2016, Sabrina Yu wrote: > > 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 > > > _______________________________________________ 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.
