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 Stǎnicǎ, 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<mailto: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<mailto: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 Stǎnicǎ, 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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