Hi,

I had problems with skullstriping. I ran recon-all and part of the skull is being considered as cortex in the segmentation. I tried to fix this using:

recon-all -skullstrip -wsthresh 50 -clean-bm -subjid <subject name>

and than

recon-all -autorecon-pial -subjid <subject name>

But nothing changed.

Do I need to run recon-all all over?

Thanks,

Mateus