Dcm2niix identifying EPI orientation incorrectly?

Software Support
,
1

Summary of what happened:

I am trying to use dcm2bids to convert some DICOMs to NIFTI format before running fmriprep. For the EPI scans, the protocol states Sagittal R >> L, Coronal A >> P, Transversal F >> H (or I >> S), and Phase Encoding Direction A >> P. Therefore, I believe the .nii file should be LPS orientation and the json file should have “PhaseEncodingDirection”: “j”
For the field maps, Sagittal R >> L, Coronal A >> P, Transversal F >> H and Phase Encoding Direction R >> L. So, should be “PhaseEncodingDirection”: “i”
However, after running dcm2bids, I get LAS as the EPI orientation and j as the pe direction, and i- as the pe direction for the field maps. I’m not sure why this is, but I’m thinking perhaps because we’re using a tilted acquisition, it’s confusing dcm2bids’ method for determining orientation. When I view the image in AFNI it seems like it’s LPS (i.e. coordinates are positive in left, posterior and superior regions), however after some reading I think this may be the way AFNI visualizes all images, is that right?
When I then run fMRIPrep, it tells me the orientation is LAS and phase encoding direction is Posterior-Anterior, but the distortion correction looks ok.

Command used (and if a helper script was used, a link to the helper script or the command generated):

dcm2bids: dcm2bids -d ${raw_dir}/${subj}/${ses}/DICOMs -p "${subj}" -s "${ses}" -c ${config_dir}/bids-config_${subj}_${ses}.json --forceDcm2niix
with config file as follows:
{
	"descriptions": [
		{
			"dataType": "anat",
			"modalityLabel": "T1w",
			"criteria": {
				"SeriesNumber": 10
			}
		},
		{
			"dataType": "fmap",
			"modalityLabel": "magnitude1",
			"intendedFor": [
			3,
			4,
			5],
			"criteria": {
				"SeriesNumber": 4,
				"EchoTime": 0.01
			}
		},
		{
			"dataType": "fmap",
			"modalityLabel": "phasediff",
			"intendedFor": [
			3,
			4,
			5],
			"criteria": {
				"SeriesNumber": 5,
				"EchoTime": 0.01476
			}
		},
		{
			"dataType": "func",
			"modalityLabel": "bold",
			"customLabels": "task-affvis",
			"criteria": {
				"SeriesNumber": 6
			},
			"sidecarChanges": {
				"TaskName": "affvis"
				}
		},
		{
			"dataType": "func",
			"modalityLabel": "bold",
			"customLabels": "task-facegender",
			"criteria": {
				"SeriesNumber": 8
			},
			"sidecarChanges": {
				"TaskName": "facegender"
				}
		},
		{
			"dataType": "func",
			"modalityLabel": "bold",
			"customLabels": "task-facememory",
			"criteria": {
				"SeriesNumber": 2
			},
			"sidecarChanges": {
				"TaskName": "facememory"
				}
		}
	]
}

Version:

dcm2bids v2.1.9

Environment (Docker, Singularity, custom installation):

Conda

Please let me know if there’s any other information that might be useful! I feel like I may be missing something important.