Fmaps, Phase Encoding Direction, and Distortion Correction


  • 2 EPI runs undergoing preprocessing with fmriprep (v22.1.1). The PE direction is PA.
  • 2 fmaps (PE direction: AP and PA) for each associated EPI run.
  • When running fmriprep, I recently learned that my field maps are mistakenly both in the same PE direction (AP). I thought to drop one of the fmaps for each EPI run to still be used by fmriprep. No errors were thrown when doing so, but the html output seems especially distorted for some participants after correction.


  1. Does it even make sense to still include a single fmap for each EPI run, given that the
    html report states "Utilizing two or more images with different phase-encoding polarities (PEPolar) or directions, it is possible to estimate the inhomogeneity of the field"?
  2. Could it be that having 2 fmaps that are the same PE direction but intended for the separate EPI runs is somehow throwing off distortion correction?

SDC from one of the EPI runs:

Any advice is greatly appreciated!

Hi @aftonnelson ,

What kind of fieldmap scans do you have in your fmap folder? Are they SE-EPI or GRE-EPI scans?

If your fieldmap scans are GRE-EPI acquisition with similar parameters than your EPI functional runs but in opposite PE direction (PA for your functional runs, AP for your fmap scans) , it should be in theory possible to correct for your EPI runs for SDC, even if in theory the best method would be to use SE_EPI scans with opposite PE direction for SDC (as GRE-EPI images are affected by both dropout and distortions whereas SE EPI images are only affected by distorsions and thus provide more accurate fieldmap estimations)

I don’t know if FMRIPREP (in fact calling SDCFlows) is able to use only one GRE-EPI image in the fmap folder with opposite PE direction than the functional image to infer the SDC through the PEPOLAR method. You need to copy one or more EPI volume(s) from the Functional run and move them to the fmap/ folder, renaming them sub-SUB...dir-PA_epi{.nii.gz/.json}.