Using reverse phase encoded B0s (DWI) for fMRIPrep distortion correction?

Software Support
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1

Summary of what happened:

Hello everyone,

I am using fMRIprep to preprocess our study’s rs-fMRI and structural images. We did not acquire fieldmaps or reverse-PE BOLD runs, but we do have reverse phase encoded B0s (one A-P, und P-A) for the DWI acquisition. I was wondering if there is a way (and if it would be advisable) to use this information or DWI preprocessing outputs (such as FSL TOPUP’s topup_field) for (non-synthetic) distortion correction of the rs-fMRI images.

SDC did work on the data, but the images still look more distorted than I would like and so if possible I would like to at least try using the acquired data instead of the estimation if possible with what I have available

I would be very grateful for any help or advice!

Best,
Jil

Command used (and if a helper script was used, a link to the helper script or the command generated):

(current fMRIprep call with synthetic distortion correction; only part of script shown)

#-----------------------------------------------------------------------------------
docker run --rm \
    -v "${BIDS}:/data:ro" \
    -v "${OUT}:/out" \
    -v "${WORK}:/work" \
    -v "${TEMPLATEFLOW}:/templateflow:ro" \
    -e TEMPLATEFLOW_HOME=/templateflow \
    "${IMG}" \
    /data /out participant \
    --participant-label "${SUB}" \
    --work-dir /work \
    --output-spaces MNI152NLin2009cAsym fsaverage5 T1w \
    --skull-strip-template MNI152NLin2009cAsym \
    --fs-license-file "${FS_LICENSE}" \
    --use-syn-sdc \
    --nthreads "${NTHREADS}" \
    --omp-nthreads "${OMP}" \
    --mem_mb "${MEM_MB}"
#-----------------------------------------------------------------------------------

Version:

fMRIprep 25.1.1.

Environment (Docker, Singularity / Apptainer, custom installation):

Docker container

Data formatted according to a validatable standard? Please provide the output of the validator:

fMRIprep relevant data is BIDS formatted and validated (anat and func); dwi folder is currently in .bidsignore as the contained b0 files were not agreeing with the BIDS validator.

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

2

Hi @jw-research and welcome to neurostars!

In this case you might be better off using something like SynBOLD-DisCo to synthesize a field map.

Best,
Steven

1 Like
3

Hi Steven, thanks a lot for the insight, and I am sorry for the late reply. I only just realized I had this stuck in drafts and hadn’t actually posted it!

Is this mainly because of me saying it seems to not be as undistorted as I’d like in my specific case, or could I generally expect a “better” outcome from SynBOLD-DisCo vs. the synthetic distortion correction implemented in fMRIprep? I’ve only used SynB0-DisCo for DWI previously.

4

Hi @jw-research,

That^

Best,

Steven

1 Like