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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.