Summary of what happened:
Objective: fMRIPRep processing of Philips fMRI resting state data along 2 Phase encoding direction. First, assuming the PhaseEncodingDirection for bold signal as j and for additional image PA as j- in fmap directory. Then, reversing the polarity in the json files and assuming j- for bold signal and j for additional image in fmap directory. The rationale for two different settings in the json file is that the Philips data does not have PhaseEncodingDirection as a filed which is inevitable for SDC using fMRIPrep.
Input data: Input directory of fmap is present in the subject directory along with func and anat which contains PEPOLAR images
Boilerplate option execution :Verbose from using –boilerplate-only option
Command used (and if a helper script was used, a link to the helper script or the command generated):
apptainer run \
--cleanenv --bind ${DATA}:/data --bind ${APP_DERIV_DIR}:/outputs \
--bind ${WORK_DIR}:/work ${APP} fmriprep /data /outputs participant \
--participant-label ${Subject} --fs-license-file ${LIC}/license.txt -w /work \
--stop-on-first-crash --debug fieldmaps --boilerplate-only --verbose --ignore slicetiming --fs-no-reconall --n-cpus 16 \
--output-spaces MNI152NLin6Asym:res-2
Version:
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Screenshots / relevant information:
fmap dir : bold signal as j and for additional image PA as j-
fmap dir : bold signal as j- and for additional image PA as j
Result : In both the instances the PEPOLAR based estimation was definitely considered in the SDC by fMRIPrep, however in both the cases the processed images seems to be same and the boilerplate verbose also suggest same combination of images considered.
Query : Why is that images from both the versions looked same ? Is the PhaseEncodingDirection has an apparent influence or the string PA in the name of the image(.nii.gz) also plays role ? Please suggest best way to edit the PhaseEncodingDirection for Philips data (in the sense how to select j and j-) in the absence of this field in the actual DICOM data?