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/
mstanica@uab.edu mailto:mstanica@uab.edu
Pronouns: she/her/hers
Image
*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! 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/ mstanica@uab.edu <mailto:mstanica@uab.edu> Pronouns: she/her/hers Image _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1upvILUH6tZ79zMXcYftS4pqQcFMtiUc2u0Q-joWUZgKCfuyy4qHr-zhg4XwZ6jBgXCYvKRl3Rc1d2bW6vaRr7--hGAXOCscil3s9N2DLjFWs9NjK38PivR2VN_HfIwzHtiB9X-VZxa4UFmG14uxzDf7TV8AMBikCNz8N4DckFhsM13iJj8uNOD0tw4oAhDXuWP3d836mNJZJ17TCiQvLs77hGjuiyt0VMr9zAKYzXdVBKImyMLAhtf8YniYvgAikz58L3yX1RRxYXl0PlxntttY15IAA0SFQn3W6ytKH6Vpp8CPsQ1kiU5kV3TxZdO4j/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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