Hi everyone,
With Bruce's extraordinary help, I've been able to get a formerly impossible subject through recon-all without error. However, the only remaining issue is that the skull strip is very strange, and is leaving too much skull at the top while simultaneously cutting off the entire cerebellum. As a result, it is also having some trouble segmenting, so I'd prefer to fix the skull strip in a way that will hopefully also fix the segmentation (see attached screenshots). I don't have any experience editing a bad skull strip that needs to have both brain added back in, and skull removed, so I'm not sure of the best order of operations. Does anyone have any suggestions? Would the best option be to use gcut for the skull and then go back in and clone the cerebellum afterwards?
Thanks!
Hayley
