Thanks @neurolabusc . Pretty sure we are. Data sorted into folders by series look like this (sequence supposed to have 37 slices):
Folder 1 : 37 dicom files (magnitude image, checked visually) – some echo 1 , some echo 2. dcm2niix detects the issue and makes “Eq” files.
Folder 2 : 37 dicome files (phase image, checked visually, but not certain whether raw phase or phasediff). dcm2niix is happy, creates e2_ph files, json has both Echo Time 1 and Echo Time 2, although I can only see one Echo Time (TE2) in the headers on all files using dicom_hdr.