In your supplied code I don't see where you calculated your T1 to FA transform, just where you calculate the inverse? Where do you get/create that original transform. And yes, using the whole head rather than the bet brain could cause problems, but that may not be your only problem. Do you have any other DTI images that are in FA space that you can use for the transform (B0, etc.)? Sometimes those other images are better for tranforming to T1 space.
-Bryson
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