Dear Freesurfeer experts,

After running the recon-all, a part of the temporal lobe of one subject was removed.

I used the watershed algorithm to be less agressive in the skull stripping step:

recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001

And the problem was solved in the brainmask.mgz volume because I can see the temporal lobe completely, but the surfaces are still displaced. In order to correct the surfaces I used the white matter edit tool but there is no change after correcting WM and running the recon-all -autorecon2-wm -autorecon3. I also used control points and but the following error was shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3:

recon-all -s sub_001 existed with errors

I detected that there are very high values in the white matter of this part of the temporal lobe (even 132), maybe it has something to do. What can I do to solve the problem with this subject?

Thank you very much in advance.

Best regards,

Marina.