Siemens Fieldmap Correction PE Direction

1

Hello,

I have multi echo fmri data (1 run, 3 echoes). I also have a Siemens field map (1 phasediff image, 2 magnitude images). I am planning on using afni to preprocess my data, but since afniproc.py cannot integrate this type of field map, I needed to field map correct separately beforehand.

The steps:

  1. Generate field map in rad/s using fsl_prepare_fieldmap
  2. Correct all 3 echoes using the field map with AFNI epi_b0_correct.py
  3. Input the three b0 corrected EPI echoes into afniproc.py

After testing it out on a few subjects I noticed the correction is not very successful. I think this is because the EPI phase encoding direction is A>>P (“j” in the .json) and the fieldmap phase encoding direction is R>>L (“i” in the .json).

In this case, I am wondering if I have to skip field map correction since it is not going to function properly with the mismatched phase-encoding planes?

Thanks in advance.