External Email - Use Caution

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