I've attached an image of the talairach.lta, which does seem to have taken a chunk out of the back of the brain.  Is this what affects the cerebellum issues?  I assume we should check this for every subject and correct it manually if necessary, but I'm confused as to how this missing chunk does not show a problem in the brainmask.mgz.  There seem to be a lot of steps and files built automatically that build on each other, and many places for things to go wrong so it's hard to tell where to look first.

Thanks for your help,
 
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> 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>
To: Jordan Pierce <jepierce87@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 <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
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