External Email - Use Caution Dear Freesurfeer experts,
After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 The problem was solved in the brainmask.mgz but not in the cortical surfaces. To handle this issue, I edited the white matter and run the recon-all -autorecon2-wm -autorecon3 without success. I also placed control points but the following error appeared after running the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I noted that white matter of this part of the temporal lobe has high values (up to 132). What can I do to solve the problem with this subject? Thank you in advance. Best regards, Marina
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