We checked and the ?h.orig surface looks right. We tried the -expert options file that you suggested anyway, but it exited with errors unfortunately and didn’t work. Is there anything else we can try?

Thanks again for your help!

Best,

Maria

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Date: Wednesday, March 6, 2024 at 9:20 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] aparc & wm underestimation

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@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

mstanica@uab.edu

Pronouns: she/her/hers
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@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!

Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64

Operating System: Red Hat Enterprise Linux 7

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

mstanica@uab.edu

Pronouns: she/her/hers
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