December 19, 2015 at 2:01 pm #139
Hi Abujamea –
It looks like a processing error happened earlier in the cortical surface extraction routine. Without seeing all of your output, my best guess is that the skull-stripping step didn’t remove a sufficient amount of the scalp/neck, which then resulted in a misclassification of GM during the tissue classification step.
Can you step through the processing steps for cortical extraction and see where if it failed there?