Note:
“PhaseEncodingAxis”: “j”,
is not equivalent to:
“PhaseEncodingDirection”: “j”,
The former is provided by dcm2niix presumably because it cannot ascertain the sign of phase encoding from the DICOM data. In the case of MRtrix3 currently, loading directly from the DICOM data would result in an absence of phase encoding information because of the inavailability of that sign information.