Here's some advice: when starting a new analysis, and especially when troubleshooting problematic code, always open up a few of the input images and make sure they are brain-shaped. Many, many hours have been spent on complicated debugging when the problem was faulty input images.
At left is a screenshot from MRIcroN, my go-to program for quickly looking at images: yep, got data in the ranges I expected and in the shape of a brain.
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