I see. The ventricles are filled in from the aseg, but if you filled in the wm.mgz that would work as well. It may not be needed though. What does it look like in a saggital view?
On Fri, 6 Feb 2009, karlkarl wrote:
Hello,
I added in an arrow to clarify. It's in the ventricle. Freesufer generatea a small circled area there, which I think should be fixed.
I tried to fix by comparing the wm.mgz and brainmask.mgz. There is no difference between wm.mgz and brainmask.mgz, no tissue left out in the wm.mgz. But for some reason, Freesurfer still generate pial/white surface in that ventricle, outlined by the red and yellow lines.
thanks
Date: Thu, 5 Feb 2009 13:23:32 -0500 From: fischl@nmr.mgh.harvard.edu To: rememberer@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter defect
can you add an arrow so it's clear what you mean? What do you mean by "here is nothing between the brainmask mgz and wm.mgz in that area".
On Fri, 6 Feb 2009, karlkarl wrote:
Hello, experts
One quick question of editing the white matter. I attached one figure
after autorecon2. In the middle of right hemisphere, there is a one small enclosed area. I would like to fill that area using the brainmask as a guide, but there is nothing between the brainmask mgz and wm.mgz in that area; so I can¡¯t paint in anything. Is this a minor defect to neglect or any other way to fix it.
Thanks a lot
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