Thanks Daniel for the explanation!

So if I understand correctly, the apparent non-alignment is due to how AFNI displays the volumes - it only looks at the scaling (diagonal elements) and translation (last column) values in the IJK_TO_DICOM_REAL matrix, right?

What I don't understand is then if I match an anatomical with an oblique EPIs using align_epi_anat.py (aligning an anatomical to an EPI, i.e. leave the EPI untouched) why visual inspection suggests that the volumes are in alignment. Since the EPIs are still oblique I would expect the alignment to be off in the AFNI viewer. Could you please explain? More generally, should I be worried that even though functional volumes seem properly aligned with an anatomical, in reality they are not?

thanks again,

Nick