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 <dgr...@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. > > [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 > listfreesur...@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-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 > https://secure-web.cisco.com/1dBhep-4JScKaeMSpTcF-8fEMe47fHnmgNQdQe8HYed1BWHIVmCDUtCar2MCbQOAs5VjKO4VET_K8UZ9gYVw6pyQcfnGPZHsZ_ji-zsU6qG9COt-LxxlwOlFA1_GhIAhp69pcg9d3vBLgjnkqGfyMJbqVw26d07kISLPMoPJpuGVkYWKNz8uMHfGEkMyprBvT1WDref94iny6MXih-CL7fWLT7LrHwCbi1FMpjuYpMM3D8ry0UFhBZnBUq9k5LFOzN2J48V47zFztq_wnG3O-7-dFCLByvLgdD4KW81X8c9J0rRAec22cygyqwQgzN5pcXn9vzWI2yOvXbOMty5tWJQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > 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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