External Email - Use Caution
Hello FreeSurfer team,
While performing QC on my recon-all output, I spotted an issue in a scan where the pial surface intersects with the white matter surface, causing distortions across several slices in that region. I overlaid the filled.mgz and white matter segmentation, and the area appears to be fully filled in both masks, so I'm not quite sure why the surfaces are inaccurate here. I'd appreciate any insights and the best way to edit this. I've attached a few example slices below for reference.
[image: image.png] [image: image.png] [image: image.png] [image: image.png]
There is no way to view surfaces properly in slices like this because the vertices exist between the slices, so they have to be projected into the slice. This can sometimes create strange images, so before we conclude that they are actually intersecting, click in the area of the intersection and then view in the sag and axial planes and see how they look.
On 8/1/2025 12:20 PM, Mahta Abbaspour wrote:
External Email - Use Caution
Hello FreeSurfer team,
While performing QC on my recon-all output, I spotted an issue in a scan where the pial surface intersects with the white matter surface, causing distortions across several slices in that region. I overlaid the filled.mgz and white matter segmentation, and the area appears to be fully filled in both masks, so I'm not quite sure why the surfaces are inaccurate here. I'd appreciate any insights and the best way to edit this. I've attached a few example slices below for reference.
image.png image.png image.png image.png
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
External Email - Use Caution
Thank you. I already looked it in 3D and from sagittal and axial views but forgot to attach those screenshots in my previous email. Please take a look at the region to the left of my cursor in the attached images.
[image: image.png] [image: image.png] [image: image.png] [image: image.png]
On Sun, 3 Aug 2025 at 16:45, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
There is no way to view surfaces properly in slices like this because the vertices exist between the slices, so they have to be projected into the slice. This can sometimes create strange images, so before we conclude that they are actually intersecting, click in the area of the intersection and then view in the sag and axial planes and see how they look.
On 8/1/2025 12:20 PM, Mahta Abbaspour wrote:
External Email - Use CautionHello FreeSurfer team,
While performing QC on my recon-all output, I spotted an issue in a scan where the pial surface intersects with the white matter surface, causing distortions across several slices in that region. I overlaid the filled.mgz and white matter segmentation, and the area appears to be fully filled in both masks, so I'm not quite sure why the surfaces are inaccurate here. I'd appreciate any insights and the best way to edit this. I've attached a few example slices below for reference.
[image: image.png] [image: image.png] [image: image.png] [image: image.png]
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1DjE_7CtUIT7gpRLAmIAR8NdVA9PTKbUzA6yseIOcd-9kNL... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/12Jt86R433fR2hqCRQnKp4SV9BTNqwq1zYu1DA9X_lWAKxM... < https://secure-web.cisco.com/12Jt86R433fR2hqCRQnKp4SV9BTNqwq1zYu1DA9X_lWAKxM... .
I can't really see what is happening (to the left of the cursor looks ok to me). Look at the filled.mgz and see if the WM seg looks weird in that area.
On 8/4/2025 1:09 PM, Mahta Abbaspour wrote:
External Email - Use Caution
Thank you. I already looked it in 3D and from sagittal and axial views but forgot to attach those screenshots in my previous email. Please take a look at the region to the left of my cursor in the attached images.
image.png image.png image.png image.png
On Sun, 3 Aug 2025 at 16:45, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
There is no way to view surfaces properly in slices like this because the vertices exist between the slices, so they have to be projected into the slice. This can sometimes create strange images, so before we conclude that they are actually intersecting, click in the area of the intersection and then view in the sag and axial planes and see how they look. On 8/1/2025 12:20 PM, Mahta Abbaspour wrote:External Email - Use Caution Hello FreeSurfer team, While performing QC on my recon-all output, I spotted an issue in a scan where the pial surface intersects with the white matter surface, causing distortions across several slices in that region. I overlaid the filled.mgz and white matter segmentation, and the area appears to be fully filled in both masks, so I'm not quite sure why the surfaces are inaccurate here. I'd appreciate any insights and the best way to edit this. I've attached a few example slices below for reference. image.png image.png image.png image.png _______________________________________________ Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ <https://secure-web.cisco.com/1DjE_7CtUIT7gpRLAmIAR8NdVA9PTKbUzA6yseIOcd-9kNLGa-vLV9gjvKWbDr2nE9eJKunm-K1anEX6JvWMFB3QuKYv4ipvQyWTn9_TF7rFMXK4-F_Icrthw0eLPPt5DE3dt2bJghxU8Zatdw1mSVwYppUi57kpT_AIbY-IMnb-v8_E4heiVDFGYdBbDnauUdp2QjPV4vs8Lg8wP5l3LPaTqFbG1Qh6ED3zm6gfTSk5BoICiC6i0EgQzjEc5PXDyg9DcyDMeH-X_JsxbSJOgcyPyzvH-GlmhwCAS-T0VgbGDerGHnCRCEogZxIXMcG-AN-2kprdHFuFzrQtL6EDANA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F>_______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ <https://secure-web.cisco.com/1DjE_7CtUIT7gpRLAmIAR8NdVA9PTKbUzA6yseIOcd-9kNLGa-vLV9gjvKWbDr2nE9eJKunm-K1anEX6JvWMFB3QuKYv4ipvQyWTn9_TF7rFMXK4-F_Icrthw0eLPPt5DE3dt2bJghxU8Zatdw1mSVwYppUi57kpT_AIbY-IMnb-v8_E4heiVDFGYdBbDnauUdp2QjPV4vs8Lg8wP5l3LPaTqFbG1Qh6ED3zm6gfTSk5BoICiC6i0EgQzjEc5PXDyg9DcyDMeH-X_JsxbSJOgcyPyzvH-GlmhwCAS-T0VgbGDerGHnCRCEogZxIXMcG-AN-2kprdHFuFzrQtL6EDANA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/12Jt86R433fR2hqCRQnKp4SV9BTNqwq1zYu1DA9X_lWAKxM8VkP3BiVhre03vXbuFo4Cox3t31DnMfEu7wcj8gQig9fUHFtEwPz0ugrCsoKno5fDCF64gdNxVMthr1BJvMecPwatglItJ6ECjXc_AnEdV1679MTAzZdv-dusQNm1KVljn_XbMyiwsk5HglxgebbcsLKkq646hm2f2SYuD5kTKrXIrGT66ndJdCJ60LijfFDBmo6m0k5JSfYvtHhHhxxh5n1eSj04qXl4-HIU8obx3o0qU8XPfjVnlkzlpXXQ0Mj6BySsOZo4Xp9Do4wCPzJTydx7zoYom8IJY0yNXwQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/12Jt86R433fR2hqCRQnKp4SV9BTNqwq1zYu1DA9X_lWAKxM8VkP3BiVhre03vXbuFo4Cox3t31DnMfEu7wcj8gQig9fUHFtEwPz0ugrCsoKno5fDCF64gdNxVMthr1BJvMecPwatglItJ6ECjXc_AnEdV1679MTAzZdv-dusQNm1KVljn_XbMyiwsk5HglxgebbcsLKkq646hm2f2SYuD5kTKrXIrGT66ndJdCJ60LijfFDBmo6m0k5JSfYvtHhHhxxh5n1eSj04qXl4-HIU8obx3o0qU8XPfjVnlkzlpXXQ0Mj6BySsOZo4Xp9Do4wCPzJTydx7zoYom8IJY0yNXwQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Mahta Abbaspour