It is worth noting that dicm2nii and dcm2niix are separate tools, so an older version of dicm2nii may perform better than a later version of dcm2niix (or vice versa). The two teams work closely together, so most should perform well for most cases, but you may observe differences for edge cases. It is worth noting that the lead developers for both tools work a sites with Siemens equipment, and therefore rely on users for exemplars for other manufacturers.
In particular, Philips users should only export to PAR/REC when required (e.g. multi band sequence with too many slices to be exported to DICOM with current Philips software). I would heed the warning of a Philips engineer that PAR/REC reflects simpler times and contains limited meta data.
As you note, dicm2nii uses the PAR tag
Preparation Direction to determine the BIDS tag
. Preparation direction : Anterior-Posterior
However, in my experience, this PAR value only reports the
PhaseEncodingAxis. In other words, it will report
Anterior-Posterior for both
Anterior->Posterior as well as
Posterior->Anterior. So while dicm2nii will respond to the value
Posterior-Anterior, I am not convinced this is ever seen in actual data. This explains why dcm2niix does not support this feature: I prefer to only include information I am confident about. You should be fine using either dicm2nii, or using dcm2niix and inserting the tag:
However, you will have to intervene if you have any FSL TOPUP compatible undistortion series which leverages reversed polarity phase encoding (which was the original rationale for the
Unfortunately, phase encoding polarity is also missing from Philips DICOM data. I urge all users of Philips equipment to lobby their Philips Research Collaboration Managers to provide critical meta data. The impoverished BIDS files created by dcm2niix and dicm2nii for Philips data is a reflection of the missing information in the source files, not in the conversion software.