I came across two subjects who had incomplete surfaces because of an aggressive skull strip. After changing the watershed parameters to include the missing brain parts and running the subject through autorecon2 and autorecon3 again, the surfaces were included for one hemisphere but not the other. 

I've attached screenshots for these subjects. For one of the subjects, I tried including control points where necessary and running autorecon2-cp, and it still didn't fix the incomplete surfaces. Any ideas on what to do next? 

Thank you!

Maia