Please tell your students that at all times, no matter what program they use, they should spend a few minutes to make sure the alignment program did a good job. Our program is pretty robust, but it still can give bad results on occasion, so it is very important to check to make sure that the image volumes are aligned the way you expect them to be.
The -AddEdge option to align_epi_anat.py is designed to create edge-enhanced datasets that can be very helpful in this visual checking step. See our paper
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afni.nimh.nih.gov]
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afni.nimh.nih.gov]
for more information!
