fMRIPrep based processing to process SDC using SyN

Software Support
,
1

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:

image
image1182Ă—347 126 KB

Query : Please suggest how we could overcome this error and successfully process the SyN based SDC ?

2

To ignore pepolar fieldmaps, use --ignore fieldmaps.

As to the error: Please retry with 25.0. This should be resolved.

1 Like
3

Thank you for the response.
I need to inform here explicitly that the second section " An attempt to invoke fMRIPrep based SyN approach for SDC --use-syn-sdc --force-syn" is processed without fmap directory at all and hence –ignore filedmaps was not included. But, we observed that the SyN based correction was started. Do you suggest to process –ignore fieldmaps in the absence of fmap directory?
Thank you for the information about the version 25.0.

4

Thank you very much for informing about the version 25.0.
The Runtime Error: Spline fit … did not arise in newer version and the SyN based SDC was successful.
I need to inform also that this was possible when the input data directory has no fmap directory.

B0 field inhomogeneity map will be estimated with the following 1 estimator(s): [<EstimatorType.ANAT: 5>]. 250417-10:51:31,543 nipype.workflow INFO: 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>250417

Thank you