I have a question regarding the skull stripping process. I ran my data through recon-all but still had much skull intact. I then followed the recommended process per the freesurfer wiki to change the watershed threshold levels on the recon process. I did so at the 20, 15, 10, 5, and 0 threshold with little improvement to the amount of skull removed. I know a similar question has been asked but in that scenario freesurfer was not including the skull as part of the cortical matter while in my scenario it is. Do you have any further suggestions as to how to remove the skull from my images? Thank you.
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