Hi,
I have an image that is completing the skull strip with a lot of skull/dura remaining and it is affecting the surfaces. I've tried lowering the watershed threshold as low as 5 and I've tried adding the -gcut option, but the low threshold by itself does not eliminate the skull and gcut not only fails to remove the dura affecting my surfaces but it removes cerebellum as well. There is enough skull/dura left that I am hesitant to try manual edits, but I don't know any other options. I believe a good source of my trouble comes from my own confusion about how much remaining dura/skull is acceptable and how much cerebellum can be missing without affecting the rest of the data. I've uploaded the file (AL.zip) to the FTP server. If anybody has the time I would greatly appreciate it if I could have it looked at. Thank you very much.
--Vincent