Hello Elena, Could you please explain what you are trying to fix by editing the white matter? Some screen shots of your data would be helpful in understanding your issue. Also, could you please specify which files you are editing, based on your description I believe you are editing the wm.mgz volume.
Information on making white matter edits can be found here on our wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 It may be worth mentioning that white matter surface segmentation is not solely dependent on the wm.mgz volume. This means that voxels with values in the wm.mgz volume are not necessarily included in the white matter surface. Best, Jackson ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Elana Sarabin <elana.sarab...@ucalgary.ca> Sent: Monday, December 28, 2020 1:32 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Erasing WM External Email - Use Caution Hello, I seem to be having two issues when erasing white matter. My first problem is that when I erase white matter and then run my fixes the voxels will show as being erased but the line that distinguishes between white matter and grey matter doesn’t re adjust so it doesn’t look like any erasing has been done. The command I use after editing the white matter is recon-all -autorecon2-wm -autorecon3 -s subj_ID . My second issue is sometimes when I go to erase white matter there is nothing to erase. Normally where there is white matter the voxels are pink, however, sometimes despite an area being encompassed by the white matter line, there is no colour underneath to erase. Any suggestions to fix these problems would be greatly appreciated. Kindest Regards, Elana
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