Hi all,
I recently read your article (Glen et al., 2020). I have a question based on it/check_flip.
I have images that were acquired in RPI orientation (verified with a vitamin E capsule. When I ran align_epi_anat.py, I get the outcome NO_FLIP (using the raw images as input). So far, so good.
However, previously, I had reoriented the mprage and epi images to RAI (as I know that is the afni default) and then deobliqued them. I reoriented them using 3drefit -orient RAI. When I use THESE Images as the input to align_epi_anat.py, the outcome is DO_FLIP.
Could you please explain why this might happen?
Thanks,
Matt
