Dear experts,

I recently finished processing a subject for whom I had performed a skull-strip on the brainmask.mgz 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 as the troubleshooting tutorial suggested to regenerate the surfaces based on the new brainmask.mgz volume:


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

However, after the subject finished processing the surfaces were generated/outlined on the dura as well. I tried performing a g-cut command but it did not get rid of the dura. I also had issues with the subcortical segmentation as the ventricles were not completely segmented.  

Thank you for your help.

Best,

Arsenije