Unbeknownst to me, I ran my preprocessing in afni (slice-time correction, EPI/anatomy alignment, and motion correction) with the EPIs in RAI orientation and the anatomical scan in RPI orientation. Yet, the alignment between EPI and anatomy looks good when I view it in the AFNI GUI. Am I to infer that AFNI can compare datasets perfectly sensibly even when their in different orientations? Or should I re-run everything? Will having datasets in different orientations screw things up for me farther down the road?
Thanks,
Dan