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:
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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> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu <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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