fmriprep: N4BiasFieldCorrection error in sbref image

Hi,

first of all, thank you for your great effort in standardizing preprocessing pipelines! For now, I am trying to run a workflow with

• 2 bold series with MB factor 3 (bad contrast)
• 1 sbref series collected before run-01 for registration with T1 (high contrast)
• 1 T1w
• 1 phasediff+ 2 magnitude fmap images.

I am not quite sure why the workflow doesn’t like my data - it fails on the bold_reference_wf.skullstrip_and_enhance_wf, specifically in the sbref N4 correction wf step. Error message below:

[Node] Error on "fmriprep_wf.single_subject_C19_wf.func_preproc_ses_01_task_wm_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" (/scratch/fmriprep_wf/single_subject_C19_wf/func_preproc_ses_01_task_wm_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct)

RuntimeError: Command:
N4BiasFieldCorrection -d 3 --input-image /scratch/fmriprep_wf/single_subject_C19_wf/func_preproc_ses_01_task_wm_run_01_wf/bold_reference_wf/validate_ref/sub-C19_ses-01_task-wm_run-01_sbref_valid.nii.gz --mask-image /scratch/fmriprep_wf/single_subject_C19_wf/func_preproc_ses_01_task_wm_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output sub-C19_ses-01_task-wm_run-01_sbref_valid_corrected.nii.gz
Standard output:

Standard error:

Return code: 1

I am also not sure I conceptually understand what is failing here - my best guess that this is a problem of correcting the reference singleband before being registered the template? Edit: I tried to run the pipeline without providing sbref images, and it looks like this way, bold images are N4 corrected and the workflow doesn’t fail. However, direct registration of MB bold to MNI looks pretty imprecise.

I would appreciate any help, as I really want to promote your pipeline as a new standard in our lab 😃

Btw, this is the exact command I ran:

docker run --rm -it -e DOCKER_VERSION_8395080871=18.09.0 -v /home/heike/Documents/Freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /home/heike/Desktop/MRI_ex:/data:ro -v /home/heike/Desktop/preproc_MRI_ex:/out -v /home/heike/Desktop/interm:/scratch poldracklab/fmriprep:1.2.5 /data /out participant --participant_label C19 -t wm --ignore slicetiming --bold2t1w-dof 6 --output-space template --no-submm-recon --fs-no-reconall --write-graph -v -w /scratch --template-resampling-grid native