I mean to tar and gzip the entire subject dir, which will be too big to email. You can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Thu, 1 Dec 2016, Rizvi, Batool wrote: > Hi Bruce, > Thanks for your reply. It is actually brighter on the brainmask.mgz than the > orig.mgz when I checked. I'm uploading the freesurfer subject here. > > Thanks! > BR > > ________________________________________ > 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, December 01, 2016 2:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity > change > > hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not > really possible to diagnose from a single slice from a single subject. If > you tar, gzip and upload the subject one of us will take a look > > cheers > Bruce > On Thu, 1 > Dec 2016, Rizvi, Batool wrote: > >> >> Hi FreeSurfer experts, >> >> >> >> After running -autorecon2 and -autorecon3, we're seeing issues for some of >> the subjects, which now start showing changes in intensity/brightness in >> some voxels, and this increased intensity is now missed by the white matter >> and grey matter segmentation, and is labeled as non-brain matter. >> >> >> >> Attached is an example of a subject's brain that was segmented incorrectly, >> which we think is due to the intensity around that frontal region. We hadn't >> added control points in that region, so we are unsure what the cause of the >> intensity change is. In our first pass before running -autorecon2 >> -autorecon3, we did not notice this error or the intensity values to be so >> bright for that region. >> >> >> >> Thanks for your help! >> >> BR >> >> >> _______________________________________________ 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.
