You can check it with: cd $SUBJECTS_DIR/$subject/mri tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca --targ brainmask.mgz --lta-inv transforms/talairach.lta --reg junk.reg.dat --s $subject
don't try to edit it though. If it is off, get back to us. doug On 04/17/2012 12:08 PM, Jordan Pierce wrote: > What should I be looking for in the talairach.lta? > Jordan Pierce > Graduate Student > Behavioral and Brain Sciences Program > Psychology Department > The University of Georgia > *From:* Bruce Fischl <fis...@nmr.mgh.harvard.edu> > *To:* Jordan Pierce <jepierc...@yahoo.com> > *Cc:* Allison Stevens Player <astev...@nmr.mgh.harvard.edu>; > Freesurfer Support <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Tuesday, April 17, 2012 9:37 AM > *Subject:* Re: [Freesurfer] Segmentation > > 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 > <mailto: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 >> <mailto:astev...@nmr.mgh.harvard.edu>> >> *To:* Jordan Pierce <jepierc...@yahoo.com <mailto:jepierc...@yahoo.com>> >> *Cc:* Freesurfer Support <freesurfer@nmr.mgh.harvard.edu >> <mailto: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 >> <mailto: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 <mailto: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 <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
