Fmriprep reporting issue of phase-encoding direction?


I am processing functional scans through fmriprep with their respective fieldmaps for susceptibility distortion correction, but fmriprep appears to be incorrectly detecting the functional scan’s phase-encoding direction when I look at the html reports after completing preprocessing.

see screenshot below from summary for a PA functional scan:

My functional scans are collected first with PA direction, then AP direction. Fieldmaps are collected prior, resulting in PA and AP fieldmaps that are intended for respective functional scans as described in the fieldmap jsons (e.g. PA field map intended for subsequent AP functional scans, and AP field map intended for subsequent PA functional scans). The jsons of the functional scans correctly describe the phase-encoding directions as “j” for PA and “j-” for AP scans, and same for the jsons of fieldmaps. Also, the orientation of the images are all RPI, and while it is indicating the wrong direction in the html report, the actual correction appears to be correct.

Has anyone encountered this issue when dealing with susceptibility distortion correction with fmriprep? Is it just a reporting issue or is there something more serious going on?


fMRIPrep currently tells you the axis, but not the polarity, so both j and j- show up as Anterior-Posterior in the report. I don’t recall the exact reason, but I don’t see any reason not to improve it now. Would you be interested in submitting a pull request?