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 fischl@nmr.mgh.harvard.edu *To:* Jordan Pierce jepierce87@yahoo.com *Cc:* Allison Stevens Player astevens@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 <jepierce87@yahoo.com mailto:jepierce87@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 <astevens@nmr.mgh.harvard.edu mailto:astevens@nmr.mgh.harvard.edu> *To:* Jordan Pierce <jepierce87@yahoo.com mailto:jepierce87@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 <jepierce87@yahoo.com mailto:jepierce87@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
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