Dear experts,

I recently finished processing a subject for whom I had performed a skullstrip on the brainmask volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following command: 

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

However, when recon was finished, I noticed that the skull re-appeared and the surfaces were outlined on it. I went back and tried g-cut to remove the little dura that was left over, but that also did not work. I tried varying the watershed parameters again but I keep getting the same result. Is there any other underlying issue that may be at fault? 

Thanks for your help,

Arsenije