Hi Catherine, if the skull strip is ok, then it might be that there were some defects that messed things up. Try running defect-segto generate segmentations of the defects. Look in the help for how to view the segmentations. doug
On 02/14/2013 03:36 PM, Rongxiang Tang wrote:
Hi Bruce,
I checked the skullstrip stage using this command: tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs....
and both of the brainmask and T1 images look fine.... the wm.mgz is problematic, with some area missing..... I was wondering if I need to manually adding control points to solve the problem.
Thanks, Catherine
*From:* Bruce Fischl fischl@nmr.mgh.harvard.edu *To:* Rongxiang Tang rongxiangtang@yahoo.com *Sent:* Thursday, February 14, 2013 2:03 PM *Subject:* Re: [Freesurfer] talairach transformation troubleshooting problem
Hi Catherine
that looks like something went wrong in the surface recon, not in the talairaching. Maybe a skullstrip problem? You need to investigate. Also, please cc the list so that others can answer!
thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote:
Hi Bruce,
I attached two images...one is the target view and the other is the
moveable
view.
Thanks, Catherine
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
To: Rongxiang Tang <rongxiangtang@yahoo.com
mailto:rongxiangtang@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, February 14, 2013 1:33 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting
problem
Hi Catherine
can you send us an image of what you are looking at?
thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote:
Dear All,
When I was checking the talairach transformation output, I noticed
that
some of the white matter was not included inside
the green line. Instead of drawing the green line to include all
of the
white matter of the whole brain, it somehow only
includes the bottom half of the white matter of the brain.
Is there a way to fix that?
Thanks, Catherine
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