This is difficult to debug remotely. The first thing to look at is the
?h.orig surface. Does that look more-or-less right? If not, then it
means that the wm.mgz is wrong. If it does not look right, it means that
the surface placement algorithm is pushing the surface into subcortical
gray. One way to overcome this is to create a
brain.finalsurfs.manedit.mgz by copying the brain.finalsurfs.mgz, then
edit the brain.finalsurfs.manedit.mgz to set those areas where the
surface is off to 255. Then create an expert options file with
WhitePreAparc --rip-bg-no-annot --restore-255 --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option
On 3/5/2024 7:10 PM, Stanica, Maria wrote:
External Email - Use Caution
Yes, the problem is that the white surface on the left side of the
image is extending too far into subcortical gray matter. We did delete
the control points and ran some white matter edits, but the image I
sent you is after we applied those edits (it was even worse before). I
don’t see any other wm edits we can make to the image. It didn’t
resolve our issue enough to make the image usable for our analyses, so
I wanted to see if there was anything else we could do to resolve the
problem.
Thank you!
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Date: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] aparc & wm underestimation
Just to make sure I understand, the problem is that the white surface
on the left side of the image is extending too far into subcortical
gray matter, right? This can be difficult to fix, but the right fix is
to edit the wm.mgz. Make sure to delete your control points as that is
not the right fix. Also, remember that the surfaces in this area may
always be inaccurate if you can see where the boundary is.
On 3/3/2024 6:09 PM, Stanica, Maria wrote:
* External Email - Use Caution *
This is after the most recent round of edits for one of the subjects.
*Maria St**ǎ**nic**ǎ**, B.A.****| **Graduate Student*
Medical/Clinical Psychology Doctoral Program
UAB |/The University of Alabama at Birmingham/
mstan...@uab.edu <mailto:mstan...@uab.edu>
Pronouns: she/her/hers
Image
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] aparc & wm underestimation
Can you send pictures of the slices showing the problem?
On 3/3/2024 3:18 PM, Stanica, Maria wrote:
* External Email - Use Caution *
Hello FS developers,
I ran my subjects through skullstripping and recon-all.
Everything processed correctly (and exited without errors),
except 4 images which have an underestimation in coronal
subcortical region. The underestimation is significant and
goes on for about 10-12 slices (for one image it was 153-162,
for another it was 150-164).
After searching the list, we attempted control points, which
ended up not working (I don’t believe this was the right
method to correct the error). Then we tried white matter
edits, and one of the images was resolved, but the other 3 did
not get better. Is there anything else we could do to try to
resolve the issue? I can provide any other information needed.
Any help would be appreciated!
1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
2. Operating System: Red Hat Enterprise Linux 7
3. OS Version: 7.9 (Maipo)
Best,
Maria
*Maria St**ǎ**nic**ǎ**, B.A.****| **Graduate Student*
Medical/Clinical Psychology Doctoral Program
UAB |/The University of Alabama at Birmingham/
mstan...@uab.edu <mailto:mstan...@uab.edu>
Pronouns: she/her/hers
Image
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