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Dear Freesurfer 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