I want to use fieldmap correction in fmriprep but I am unsure how to correctly specify phase encoding direction in the .json files for fMRI data according to BIDS. We are working on a Philipps Scanner and according to our MR-physicist the phase encoding direction for our sequence is Anterior-Posterior. When I check the nifti-file header (using fslhd), the second axis is indicated as “qform_yorient: Posterior-to-Anterior” (same for sform_yorient). Does this mean that I have to indicate the phase encoding direction as “j-” ?
Thanks for your help.
Official BIDS specification for phase encoding direction: “Possible values:
"k-". The letters
k correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless
- sign is present (then the order is reversed - starting from the highest index instead of zero)”