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.