External Email - Use Caution
Dear FreeSurfer Team,
We are editing some longitudinal data using FreeSurfer 7.4.1. I am not sure how to fix the following issue (see the attached pictures). The white surface (blue line) almost touches the pial surface because some of the voxels are "too bright" at the edge, so they were misidentified as white matter.
[image: Screenshot 2025-01-21 at 1.21.23 PM.png] [image: Screenshot 2025-01-21 at 1.21.32 PM.png]
Which volume should I edit to fix this? I was thinking about deleting these voxels from the brainmask but that might lead to excluding/deleting gray matter incorrectly. Or maybe I could delete these voxels from the white matter. I was also considering cloning some of the surrounding voxels somehow to make this area less bright.
Thank you, Eszter
You can edit the brain.finalsurfs.manedit.mgz to remove those voxels. You may need to removed them from the wm.mgz and filled.mgz
On 1/21/2025 1:41 PM, Eszter Boros wrote:
External Email - Use Caution
Dear FreeSurfer Team,
We are editing some longitudinal data using FreeSurfer 7.4.1. I am not sure how to fix the following issue (see the attached pictures). The white surface (blue line) almost touches the pial surface because some of the voxels are "too bright" at the edge, so they were misidentified as white matter.
Screenshot 2025-01-21 at 1.21.23 PM.png Screenshot 2025-01-21 at 1.21.32 PM.png
Which volume should I edit to fix this? I was thinking about deleting these voxels from the brainmask but that might lead to excluding/deleting gray matter incorrectly. Or maybe I could delete these voxels from the white matter. I was also considering cloning some of the surrounding voxels somehow to make this area less bright.
Thank you, Eszter
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you! So, I followed your suggestion and I edited the wm.mgz, filled.mgz, and the brain.finalsurfs.manedit.mgz. First, I got this result (see the attached picture below) which I was happy about.
[image: image.png] But the next time, when I edited the data the same way using another participant, I received this:
[image: Screen Shot 2025-02-03 at 1.49.59 PM.png]
My question is: how can I make the red line/pial surface not stop "too early" and reach the edge? I just want to delete the wrongly categorized white matter voxels and make them belong to the gray matter. I think when I edit/delete the wm voxels in the brain.finalsurfs.manedit.mgz, that stops the pial surface but that did not happen on the first figure. I am not sure what caused the difference.
Also, sometimes even when I delete/edit the white matter, the white matter surface/blue line still does not change. Am I doing something wrong with recon-all maybe? (I use recon-all -autorecon2-wm -autorecon3) [image: Screen Shot 2025-02-03 at 2.28.55 PM.png]
Thank you again!
Douglas N. Greve dgreve@mgh.harvard.edu ezt írta (időpont: 2025. jan. 23., Cs, 8:37):
You can edit the brain.finalsurfs.manedit.mgz to remove those voxels. You may need to removed them from the wm.mgz and filled.mgz
On 1/21/2025 1:41 PM, Eszter Boros wrote:
External Email - Use CautionDear FreeSurfer Team,
We are editing some longitudinal data using FreeSurfer 7.4.1. I am not sure how to fix the following issue (see the attached pictures). The white surface (blue line) almost touches the pial surface because some of the voxels are "too bright" at the edge, so they were misidentified as white matter.
[image: Screenshot 2025-01-21 at 1.21.23 PM.png] [image: Screenshot 2025-01-21 at 1.21.32 PM.png]
Which volume should I edit to fix this? I was thinking about deleting these voxels from the brainmask but that might lead to excluding/deleting gray matter incorrectly. Or maybe I could delete these voxels from the white matter. I was also considering cloning some of the surrounding voxels somehow to make this area less bright.
Thank you, Eszter
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1iTlb2rV9T0kETngpDiN1WuYhGk32CPAWdHEGYfyg-CdsyQ... 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/1dBhep-4JScKaeMSpTcF-8fEMe47fHnmgNQdQe8HYed1BWH... < https://secure-web.cisco.com/1dBhep-4JScKaeMSpTcF-8fEMe47fHnmgNQdQe8HYed1BWH... .
That is a harder problem. I'm not sure what is causing that bright spot. Artery? B0? The problem is that it is too bright and the algorithm says "hey, that's not gray matter" and does not know what to do. You can edit the voxel intensities in the brainmask.finalsurfs.manedit to darken them so they look like cortex. I think it should work but not sure
On 2/3/2025 2:37 PM, Eszter Boros wrote:
External Email - Use Caution
Thank you! So, I followed your suggestion and I edited the wm.mgz, filled.mgz, and the brain.finalsurfs.manedit.mgz. First, I got this result (see the attached picture below) which I was happy about.
image.png But the next time, when I edited the data the same way using another participant, I received this:
Screen Shot 2025-02-03 at 1.49.59 PM.png
My question is: how can I make the red line/pial surface not stop "too early" and reach the edge? I just want to delete the wrongly categorized white matter voxels and make them belong to the gray matter. I think when I edit/delete the wm voxels in the brain.finalsurfs.manedit.mgz, that stops the pial surface but that did not happen on the first figure. I am not sure what caused the difference. Also, sometimes even when I delete/edit the white matter, the white matter surface/blue line still does not change. Am I doing something wrong with recon-all maybe? (I use recon-all -autorecon2-wm -autorecon3) Screen Shot 2025-02-03 at 2.28.55 PM.png
Thank you again!
Douglas N. Greve dgreve@mgh.harvard.edu ezt írta (időpont: 2025. jan. 23., Cs, 8:37):
You can edit the brain.finalsurfs.manedit.mgz to remove those voxels. You may need to removed them from the wm.mgz and filled.mgz On 1/21/2025 1:41 PM, Eszter Boros wrote:External Email - Use Caution Dear FreeSurfer Team, We are editing some longitudinal data using FreeSurfer 7.4.1. I am not sure how to fix the following issue (see the attached pictures). The white surface (blue line) almost touches the pial surface because some of the voxels are "too bright" at the edge, so they were misidentified as white matter. Screenshot 2025-01-21 at 1.21.23 PM.png Screenshot 2025-01-21 at 1.21.32 PM.png Which volume should I edit to fix this? I was thinking about deleting these voxels from the brainmask but that might lead to excluding/deleting gray matter incorrectly. Or maybe I could delete these voxels from the white matter. I was also considering cloning some of the surrounding voxels somehow to make this area less bright. Thank you, Eszter _______________________________________________ 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/1iTlb2rV9T0kETngpDiN1WuYhGk32CPAWdHEGYfyg-CdsyQw-ttiZq903Ohut5lihvGLqpa0yjZpHKZhT1j0pDSl3uy5-7vBEYOlgWLMQxaCqYWt7mrcf_reg34QqgV_xCc-DDHKxG3mtuBJQJLj_hR0ej5zGi-LZ6OMvAzkHJHLDKmi74bPfP834R4NPepbHWYXmCNulYZWmGpVU40j7_oouV1DXYm5YNQzqEhi0Uwcyr73QA8wcJ6BVFMfd8dX5Ls58Z6VjUXE8J38NSrwxQE2QSE_IoF-CY20P-vesnS_IbPSDKPlQbuSYEuOlvaNs6fdQ9wrvBjin3_AOGcoYYQ/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/1iTlb2rV9T0kETngpDiN1WuYhGk32CPAWdHEGYfyg-CdsyQw-ttiZq903Ohut5lihvGLqpa0yjZpHKZhT1j0pDSl3uy5-7vBEYOlgWLMQxaCqYWt7mrcf_reg34QqgV_xCc-DDHKxG3mtuBJQJLj_hR0ej5zGi-LZ6OMvAzkHJHLDKmi74bPfP834R4NPepbHWYXmCNulYZWmGpVU40j7_oouV1DXYm5YNQzqEhi0Uwcyr73QA8wcJ6BVFMfd8dX5Ls58Z6VjUXE8J38NSrwxQE2QSE_IoF-CY20P-vesnS_IbPSDKPlQbuSYEuOlvaNs6fdQ9wrvBjin3_AOGcoYYQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1dBhep-4JScKaeMSpTcF-8fEMe47fHnmgNQdQe8HYed1BWHIVmCDUtCar2MCbQOAs5VjKO4VET_K8UZ9gYVw6pyQcfnGPZHsZ_ji-zsU6qG9COt-LxxlwOlFA1_GhIAhp69pcg9d3vBLgjnkqGfyMJbqVw26d07kISLPMoPJpuGVkYWKNz8uMHfGEkMyprBvT1WDref94iny6MXih-CL7fWLT7LrHwCbi1FMpjuYpMM3D8ry0UFhBZnBUq9k5LFOzN2J48V47zFztq_wnG3O-7-dFCLByvLgdD4KW81X8c9J0rRAec22cygyqwQgzN5pcXn9vzWI2yOvXbOMty5tWJQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1dBhep-4JScKaeMSpTcF-8fEMe47fHnmgNQdQe8HYed1BWHIVmCDUtCar2MCbQOAs5VjKO4VET_K8UZ9gYVw6pyQcfnGPZHsZ_ji-zsU6qG9COt-LxxlwOlFA1_GhIAhp69pcg9d3vBLgjnkqGfyMJbqVw26d07kISLPMoPJpuGVkYWKNz8uMHfGEkMyprBvT1WDref94iny6MXih-CL7fWLT7LrHwCbi1FMpjuYpMM3D8ry0UFhBZnBUq9k5LFOzN2J48V47zFztq_wnG3O-7-dFCLByvLgdD4KW81X8c9J0rRAec22cygyqwQgzN5pcXn9vzWI2yOvXbOMty5tWJQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
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Douglas N. Greve -
Eszter Boros