I have data collected in a HCP-like style with pairs of functional runs collected with opposite encoding direction. They are of equal length (102 volumes), e.g. sub-OA01/func/sub-OA01_task-control_acq-MB_dir-AP_run-01_bold.nii.gz & sub-OA01/func/sub-OA01_task-control_acq-MB_dir-PA_run-02_bold.nii.gz. I am unclear on how to modify the json files so that PEPOLAR distortion will run in fmriprep. I came across this post: Fmriprep test data with fieldmap, but I’m not sure how to adapt it.
Since fmriprep.workflows.fieldmap.pepolar.init_pepolar_unwarp_wf is looking for a epi should I do the following?
- extract the first 10 or so volumes from the AP and PA bold runs, save these as something like sub-OA01/fmap/sub-OA01_acq-control_dir-AP_epi.nii.gz
- modify the json to read “IntendedFor”: “func/sub-OA01/func/sub-OA01_task-control_acq-MB_dir-PA_run-02_bold.nii.gz”
- Similar to 2, but for the bold AP run have a PA epi