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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 mstanica@uab.edumailto:mstanica@uab.edu Pronouns: she/her/hers [Image]
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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edumailto: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 Stǎnicǎ, B.A. | Graduate Student Medical/Clinical Psychology Doctoral Program UAB |The University of Alabama at Birmingham mstanica@uab.edumailto:mstanica@uab.edu Pronouns: she/her/hers [Image]
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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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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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.edumailto:mstanica@uab.edu Pronouns: she/her/hers [Image]
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Sunday, March 3, 2024 at 3:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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 mstanica@uab.edumailto:mstanica@uab.edu Pronouns: she/her/hers [Image]
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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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 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> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@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/ 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> _______________________________________________ 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/1NtCKu7oOBr2RU1c0qeu8omZiOywMqLH-BGYNz2pXBqxxByZL70MClDFuF13Xa_J8c4T5LCU0K-ULGP3-QYvzJliMh9x3KeDy0LCbKYu7J-Q7O5Y4fry1NEvEQMnmNgvtB7TlZAuz208Q_cuVNoToIcdbfCi8vre8gjcstMl_z4yGxELmjV2oanOvxeM67HYmo8tTsm4DGtpBVLN-lRHq-DC13mn_eWHbRXWyTz73o9HrHlLzosJMpTbjN0NQhl8KUOHdRVHAVyuuwjlUbVSKAa5saTIhAEOK214uhkGlNVHgRbeSQS9zva5CRhtkxAnrbuKfvJlP8ZaARJkW_Rff-w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Tuesday, March 5, 2024 at 9:11 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:mstanica@uab.edu Pronouns: she/her/hers [Image]
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Sunday, March 3, 2024 at 3:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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 mstanica@uab.edumailto:mstanica@uab.edu Pronouns: she/her/hers [Image]
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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-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> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@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/ 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> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@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/ 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> _______________________________________________ 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/1NtCKu7oOBr2RU1c0qeu8omZiOywMqLH-BGYNz2pXBqxxByZL70MClDFuF13Xa_J8c4T5LCU0K-ULGP3-QYvzJliMh9x3KeDy0LCbKYu7J-Q7O5Y4fry1NEvEQMnmNgvtB7TlZAuz208Q_cuVNoToIcdbfCi8vre8gjcstMl_z4yGxELmjV2oanOvxeM67HYmo8tTsm4DGtpBVLN-lRHq-DC13mn_eWHbRXWyTz73o9HrHlLzosJMpTbjN0NQhl8KUOHdRVHAVyuuwjlUbVSKAa5saTIhAEOK214uhkGlNVHgRbeSQS9zva5CRhtkxAnrbuKfvJlP8ZaARJkW_Rff-w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ 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/1-s0isuaXwSLBRN1xMd8QzSL5bR3YMcQIJYdhk7Wddctq55nLH85tRNWQRKmOW6xg9E9iefjMG5Q8KR4EXFJdvTHyoWPS2grcuZj6f8A7dqzDIc6lxN_t63Qfrvx5BlgN47jQFwnXYixe0WZW4mB2hznES5uoR5aEWMkMu1LQzEJEsdG6C2Uk-ABvt4tRlC0fsKlYQExO1Va8JlMLye_cww4D04eLzJdcqUUyUFU05nv-AySaAxrd6eaD4dua2FTXWanUEOv5VtmXKT1Fq9iYtTT-NTVn8gx0mr3-aChJR-H6Og6MayROlDtbiLpxo2-VHTjFTichTBb6-rqemRYiLA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Stanica, Maria