https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1607&L=fsl&D=0&P=336137
Here is a very similar case. In summary, it seems like the issue wasn't solved, however it was reported that "the median intensity in the brain mask [was] 0. I'm using 2 AFNI commands for skullstripping and mask application. In FSL viewer (and fslhd), the brain-extracted output looks ok. All input images (EPI, lowres, highres, Template) are skull brain-extracted.
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