afni.nimh.nih.gov

So why all the warnings? Any fMRI practitioner knows that for two scans to be aligned, you have to align them. And yet AFNI makes it seem like something's wrong with the data and extreme measures must be taken if two datasets don't start out aligned.

Also, align_epi_anat.py does not put the anatomical and EPI scans in the same orientation. If one starts out RPI and the other RAI, they'll be the same after align_epi_anat.py has run.