I've also posted in the past on a set of "expert options" that helped our surfaces in the temporal lobe considerably.  You should be able to locate that post in the archives.

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO  63110 Email: mharms@wustl.edu

From: Yizhou Ma <ym850@nyu.edu>
Date: Wednesday, May 22, 2013 2:30 PM
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Cc: freesurfer <freesurfer@nmr.mgh.harvard.edu>, Chris Watson <Christopher.Watson@childrens.harvard.edu>

Subject: Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?

Ok. I'll give it a try. Thanks, Chris & Bruce!

On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Cherry

Chris is right. Putting control points in the WM will help the pial surface as well.

cheers
Bruce

On Wed, 22 May 2013, Yizhou Ma wrote:

Hi Chris,
Thanks a lot. I agree that control points should actually only be put in
white matter. I'm just not sure if I can expand the pial surface to a
satisfactory extend if I only do edits in the white matter. It seems to me
that the problem here is that the signal weakened in the lower part of the
brain so that the gray matter doesn't have adequate intensity to be included
in the pial surface (the values are around 30).

Thanks,
Cherry


On Wed, May 22, 2013 at 3:14 PM, Chris Watson
<Christopher.Watson@childrens.harvard.edu> wrote:
      You need to place the control points in the white matter, not
      around it.

      On 05/22/2013 03:04 PM, Yizhou Ma wrote:
      Dear FS experts,
I have a subject where large portions of temporal lobe is not
included in the pial surface. A member in my lab has suggested
edits on brain.finalsurfs.mgz. However, in the following page it
is indicated that edits on brain.finalsurfs.mgz is only intended
for cases regarding inclusion of cerebellum. Can anyone please
let me know which volume I should be working on in this case?

http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits

Thanks,
Cherry


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