Hello Freesurfer Experts, I'm trying to troubleshoot a problem where the main surface in our brains is not adjusting following white matter edits using Freesurfer 5.3. To be clear, the procedure here is:
1) Make edits to wm.mgz 2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3 Following this process, what we see is that the main surface in the brain still encompasses areas that were deleted from wm.mgz. Here is an example (at bottom of the inferior temporal lobe): [Inline image 1] This seems to be true for all the edits we've made on this set of brains. There are no errors in recon-all.log, and the right brain is being recon'd. Files in the surf directory seem to be updated as expected. Any idea what we're missing here? We haven't had trouble with this process in the past. Any help would be much appreciated! Thanks, Kate
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