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> 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
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