Query Regarding Field map Setup for Dual Echo GRE in BIDS Format for fMRIPrep

Software Support
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1

Hi fMRIPrep Community,

I’m working with fMRIPrep on a dataset that includes dual-echo gradient echo (GRE) field maps and have encountered an issue with distortion correction. Here’s my data setup:

Fieldmap Files:

  • Phase-difference field map: This is in Hz, and the corresponding .json file has "ImageType": ["ORIGINAL", "PRIMARY", "OTHER", "FIELDMAPHZ"].

  • Magnitude field map: The .json file has "ImageType": ["ORIGINAL", "PRIMARY", "OTHER", "MAGNITUDE"].

Functional Data: I have an EPI functional sequence, organized separately in BIDS format.

BIDS Organization for fmap:
fmap/sub-BACPAC0101002x01_magnitude_epi.json (magnitude field map)
fmap/sub-BACPAC0101002x01_phasediff_epi.json (phase-difference field map)

I have correctly filled the IntendedFor field in each of the fmap.json files, pointing to the respective functional file.

Despite this, fMRIPrep does not appear to be using the field maps for distortion correction. Could you please advise on how to get fMRIPrep to apply the precomputed field maps for susceptibility distortion correction?

Is there a specific configuration or modification needed in the BIDS structure or fMRIPrep command?

Additionally, does fMRIPrep automatically align the fieldmap with the functional file as part of its processing workflow, or is there a separate step required for this?

Thank you for your help!

Best regards,

Mahta

2

Hi @mahta.karimpoor,

These are not valid names. Please follow these naming conventions: Magnetic Resonance Imaging - Brain Imaging Data Structure 1.10.0

Additionally, it would help to show your IntendedFor and example subject tree directory to confirm you are doing it correct.

I would also provide the other information requested in the Software Support template (which you should not delete in your next post). That includes your code, software version, and BIDS validator output.

Best,
Steven