Hello,

I have used dcm2niix (v1.0.20210317) to convert ADNI DWI data collected on Siemens, GE, and Philips scanners to NIFTI format. I am trying to determine the phase encoding direction of each scan to use the eddy tool for distortion correction. 

I am aware from a post on neurostars that only the phase encoding axis can be estimated for Philips (i,j,k) but not the polarity due to missing information from meta-data (https://neurostars.org/t/bids-fmriprep-s...). So it seems, I will have to get that information from ADNI, rather than the JSON files.

For the Siemens and GE files, a majority of phase encoding directions are "j", but some are noted as "j-" in the JSON files. Given that this is an axial acquisition, "j" should map onto the y-axis (PA). I then used fslhd to confirm this by extracting the sform_code and sform_yorient information. For all subjects (regardless of whether PhaseEncodingDirection was coded as j or j-), the sform_yorient is Posterior-to-Anterior. 

For subjects with reverse polarity ("j-"), should the sform_yorient instead be coded as Anterior-to-Posterior? Ultimately, I'm wondering if there is any information from fslhd that should code the change in acquisition polarity (e.g., "j-" swapped PE direction)?

Thank you,

Jenna