Skullstripping by modifying the watershed parameter either leaves too much skull or removes entire chunks of the brain in this Siemens image; unfortunately there seems to be no middle ground.

In recon-all FreeSurfer has been unable to discern the gray matter boundary in the posterior of the brain and omits folding detail of the sulci. I am attaching a screenshot overview of the "best" attempt so far, which finished this morning (there is a bit of skull left over on this run; on previous runs where the skull is cleanly removed this problem persists). As a last-ditch effort I had re-sliced the axis-reformat T1 images as additional images (002.mgz, 003.mgz, 004.mgz) (any feedback on the feasibility of this approach is welcomed also).