Summary of what happened:
Objective: fMRIPRep with the option --ignore fieldmaps --force-syn --boilerplate-only is attempted so as to perform SDC using SyN based approach
Input data: Input directory of fmap is present along with func and anat in the subject directory which contains PEPOLAR images and hence --ignore fieldmaps is used in order to ignore the presence of field maps and thereby invoke the SyN based SDC
Result : The above options resulted in invoking EstimatorType.PEPOLAR, whereas we assumed it would invoke SyN based SDC using T1W images
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
--ignore fieldmaps
--force-syn
--verbose --ignore slicetiming --fs-no-reconall --n-cpus 16 \
--output-spaces MNI152NLin6Asym:res-2
Version:
Environment (Docker, Singularity / Apptainer, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
Setting-up fieldmap "auto_00000" (EstimatorType.PEPOLAR) with <sub-r01sub17_ses-1_dir-PA_run-01_epi.nii.gz, sub-r01sub17_ses-1_task-rest_run-01_bold.nii.gz>
250410-10:44:28,510 nipype.workflow INFO:
No single-band-reference found for sub-r01sub17_ses-1_task-rest_run-01_bold.nii.gz.
Query : Please suggest how we could successfully process the SyN based SDC by ignoring the presence of field maps (fmap dir)?
An attempt to invoke fMRIPrep based SyN approach for SDC --use-syn-sdc --force-syn
Rationale for using both the options --use-syn-sdc --force-syn is that this resulted in invoking the desired field map correction approach i.e., using T1W based SyN in the absence of additionally acquired field maps for fMRI-based processing (no fmap dir)
Attempt 1 : using --boilerplate-only
Boilerplate option execution :Verbose from using –boilerplate-only option to determine if SyN based correction is invoked
Setting-up fieldmap “auto_00000” (EstimatorType.ANAT) with <sub-r01sub17_ses-1_T1w.nii.gz, sub-r01sub17_ses-1_task-rest_run-01_bold.nii.gz>
250411-15:08:38,531 nipype.workflow INFO:
No single-band-reference found for sub-r01sub17_ses-1_task-rest_run-01_bold.nii.gz.
Result : From the above it is clear that these options has resulted in possible invoking of the SyN based correction using T1W images
Attempt 2 : using the options --use-syn-sdc --force-syn to perform SDC correction using SyN based approach of fMRIPrep
Result : The processing was completed but with the following error
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE
Screenshots / relevant information:
Query : Please suggest how we could overcome this error and successfully process the SyN based SDC ?