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