Field Maps and Phase Encoding Direction

1

Greetings,

I have an AP field map that has an IntendedFor field pointing to an AP bold scan(“PhaseEncodingDirection” : “j-”) and a PA bold scan(“PhaseEncodingDirection” : “j”). fmriprep 21.0.1 did not give me any errors. Does this mean that this field map will be used for both bold scans? From my understanding an AP field map can only be used for distortion correction on PA bold scans.

In the json sidecar fmap/sub-1104_dir-AP_run-01_epi.json I have the following:

"IntendedFor":[
"func/sub-1104_task-rest_run-02_bold.nii.gz" =======> “PhaseEncodingDirection” : “j”
"func/sub-1104_task-rest_run-01_bold.nii.gz" =======> “PhaseEncodingDirection” : “j-”
]

Thank you,
Yonatan

2

You definitely won’t be able to correct the AP scan, and I’m pretty sure fMRIPrep will not try to. It should try to correct the PA scan using the AP fieldmaps. The question on the AP scan is probably whether it will throw an error, a warning, or silently refuse to correct it. I hope it’s not silent, but I can’t immediately work through the logic (from memory).