p.s. you also have topological defects there, which you can tell as the orig (green) surface doesn't follow the voxels in the wm.mgz. The interventions Khoa suggests should help this as well. If you are missing that much wm you probably want to use control points.
cheers Bruce
On Thu, 15 Sep 2011, Khoa@nmr.mgh.harvard.edu wrote:
Hi Jing,
You have some white matter voxels missing in the wm.mgz for the rh. You can add some wm to that volume using the edit tool or you can also try control points. If you are adding wm, make sure you select the aux volume on the brush info toolbox. Fill in wm voxels for all slices. Control points would help with extending the pial surf on the lh.
-Khoa
Hi Bruce and Sita:
Thanks for your relay. And Here are the images.
Jing
From: Jing Ming [mj_coming@hotmail.com]
Sent: Thursday, September 15, 2011 7:31 PM
To: Vy Dinh
Subject: FW: [Freesurfer] manual editting problem
CC: mj_coming@hotmail.com; jennifer_g_goldman@rush.edu; vydinh@rush.edu; freesurfer@nmr.mgh.harvard.edu
From: fischl@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] manual editting problem
Date: Thu, 15 Sep 2011 20:07:41 -0400
To: sita@nmr.mgh.harvard.edu
Can you send an image?
On Sep 15, 2011, at 6:38 PM, Sita Kakunoori sita@nmr.mgh.harvard.edu wrote:
How does the wm.mgz look. Correcting the white surface will correct
the
pial surface as well.
Sita.
On Thu, 15 Sep 2011, Jing Ming wrote:
Hi Surfers:
We have been coming
across several gray matter regions that are not included within the
pial
surface (red line) when it should be (e.g., very anterior parts of
the
temporal lobe). From my understanding of similar posts on the forum,
it
seems that there isn't a way to add this region to the pial surface
so
that the missing brain matter is included. We have tried using the
clone
tool to fill in this region, as per the tutorial and have
experimented
with this tool using the tutorial data. I followed the steps in the
tutorial but could not observe any changes when the middle button was
selected. Does anyone have any ideas on how to troubleshoot this
issue? Can someone please explain to me why this is not possible?
Also
how does Freesurfer determine what regions to include within the pial
surface? If there is a way that has been developed recently, please
enlighten me.
-Jing
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