Hi Jordan That's pretty bad and means something's went radically wrong pretty early in the process. Have you checked the talairach.lta?
Cheers Bruce On Apr 17, 2012, at 8:31 AM, Jordan Pierce <jepierc...@yahoo.com> wrote: > Is there a way to only get the stats from the -aseg file that we edited > without rebuilding everything? For example, I edited a subject yesterday and > ran the -make all option, but the reconstruction changed everything in -aseg > so cerebellum is marked as grey and white matter (see attached). Do we just > have keep repeating this step until it gets it right? > > Jordan Pierce > Graduate Student > Behavioral and Brain Sciences Program > Psychology Department > The University of Georgia > From: Allison Stevens Player <astev...@nmr.mgh.harvard.edu> > To: Jordan Pierce <jepierc...@yahoo.com> > Cc: Freesurfer Support <freesurfer@nmr.mgh.harvard.edu> > Sent: Monday, April 16, 2012 3:21 PM > Subject: Re: [Freesurfer] Segmentation > > Hi Jordan, > I'm not sure I understand your question. If you run -make all, it will run > recon-all again starting at the earliest step in which there are files that > were changed that affect that step. It will run all the way through to the > end as each step affects the next one. This will change your stats which are > produced in autorecon3. > Allison > > On Apr 16, 2012, at 10:28 AM, Jordan Pierce <jepierc...@yahoo.com> wrote: > >> Hi, >> >> We're trying to edit the aseg segmentation and reconstruct it. If we run >> 'recon-all -s subject -make all' does that depend on any information from >> the surfaces or brainmask volume, or are the stats independent of that? >> >> Thank you, >> >> Jordan Pierce >> Graduate Student >> Behavioral and Brain Sciences Program >> Psychology Department >> The University of Georgia >> _______________________________________________ >> 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. > > > <freesurfer.png> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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