Oh, I see you are using 7.1.1. You can upgrade to 7.4.1. This will not
change the basic recon-all output and you'll have access to those new
features.
On 3/16/2024 4:21 PM, Stanica, Maria wrote:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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-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: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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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