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I noticed some alignment issues with one of my datasets, and I think (though am absolutely unsure) that the issue might be because the bottom-most portion of the cerebellum was cut off in the original acquisition. Aside from that, the original EPI and anatomical datasets line up pretty well, which is why I was surprised to get the misaligned output at the end of preprocessing. Are there any program options that you would suggest to help fix this, if it is possible at all? Thank you!