One thing to be aware of, your PhaseEncodingAxis will be the same regardless of the PhaseEncodingDirection. IIRC there is a vendor that won’t include the direction in the dicom files so you need to know which direction you collected based on the sequence name. As @Steven mentioned, if you’re intending to do distortion correction using AP/PA acquisitions you’ll need to figure out which is which and add the correct PhaseEncodingDirection to their sidecars. One of them will be j-
@mattcieslak is correct: PhaseEncodingAxis does not discriminate between A->P and P->A, nor does it discriminate between L->R and R->L. So for Axial scans it tells you either L?R or A?P. This is a limitation of Philips DICOM files, not dcm2niix. I would suggest that you work with the Philips Clinical Scientist associated with your center to develop a robust method for discriminating these (e.g. appending polarity to user-editable protocol names).