Fmriprep: error: argument --participant_label/--participant-label: expected at least one argument

fmriprep
#1

Dear experts,

I am trying to launch fmriprep-docker with the following command:

fmriprep-docker --participant_label 002S5018 \
>                 -vvv \
>                 --low-mem \
>                 --ignore slicetiming \
>                 --output-space {T1w,template,fsaverage} \
>                 --use-aroma \
>                 --use-syn-sdc \
>                 --write-graph \
>                 --stop-on-first-crash \
>                 -w /Users/mattvan83/fMRIprep/WD \
>                 --fs-license-file /Users/mattvan83/fMRIprep/license.txt \
>                 /Users/mattvan83/fMRIprep/BIDS /Users/mattvan83/fMRIprep/Preproc {participant}
Warning: <8GB of RAM is available within your Docker environment.
Some parts of fMRIPrep may fail to complete.
Continue anyway? [y/N]y
RUNNING: docker run --rm -it -v /Users/mattvan83/fMRIprep/license.txt:/opt/freesurfer/license.txt:ro -v 002S5018:/data:ro -v /Users/mattvan83/fMRIprep/WD:/scratch poldracklab/fmriprep:1.0.11 /data participant --participant_label -vvv --low-mem --ignore slicetiming --output-space T1w template fsaverage --use-aroma --use-syn-sdc --write-graph --stop-on-first-crash /Users/mattvan83/fMRIprep/BIDS /Users/mattvan83/fMRIprep/Preproc {participant} -w /scratch
usage: fmriprep [-h] [--version]
                [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                [-t TASK_ID] [--debug] [--nthreads NTHREADS]
                [--omp-nthreads OMP_NTHREADS] [--mem_mb MEM_MB] [--low-mem]
                [--use-plugin USE_PLUGIN] [--anat-only]
                [--ignore-aroma-denoising-errors] [-v]
                [--ignore {fieldmaps,slicetiming} [{fieldmaps,slicetiming} ...]]
                [--longitudinal] [--t2s-coreg] [--bold2t1w-dof {6,9,12}]
                [--output-space {T1w,template,fsnative,fsaverage,fsaverage6,fsaverage5} [{T1w,template,fsnative,fsaverage,fsaverage6,fsaverage5} ...]]
                [--force-bbr] [--force-no-bbr]
                [--template {MNI152NLin2009cAsym}]
                [--output-grid-reference OUTPUT_GRID_REFERENCE]
                [--template-resampling-grid TEMPLATE_RESAMPLING_GRID]
                [--medial-surface-nan] [--use-aroma]
                [--skull-strip-template {OASIS,NKI}] [--fmap-bspline]
                [--fmap-no-demean] [--use-syn-sdc] [--force-syn]
                [--fs-no-reconall] [--no-submm-recon] [--fs-license-file PATH]
                [-w WORK_DIR] [--resource-monitor] [--reports-only]
                [--run-uuid RUN_UUID] [--write-graph] [--stop-on-first-crash]
                bids_dir output_dir {participant}
fmriprep: error: argument --participant_label/--participant-label: expected at least one argument

Although my first fmriprep-docker command specifies one participant_label, the converted docker command below doesn’t seem to take into account this field.

Could anybody help me ?

Thanks !

Matt

#2

A couple of things:

  • Positional arguments should go first
  • Curly brackets indicate “options to chose from” and should not be included in the command line

So this should work:

fmriprep-docker /Users/mattvan83/fMRIprep/BIDS /Users/mattvan83/fMRIprep/Preproc participant \
                 --participant_label 002S5018 \
                 -vvv \
                 --low-mem \
                 --ignore slicetiming \
                 --output-space T1w template fsaverage \
                 --use-aroma \
                 --use-syn-sdc \
                 --write-graph \
                 --stop-on-first-crash \
                 -w /Users/mattvan83/fMRIprep/WD \
                 --fs-license-file /Users/mattvan83/fMRIprep/license.txt

I admit that the documentation and error messages could be more clear.

#3

Hi everyone,

I have a question related to this it seems fmri-prep is unable to find my participant while my bids-validated subject folder (sub-01) really is there:

iMac-van-me:~ marloulasschuijt$ /Users/marloulasschuijt/.local/bin/fmriprep-docker --low-mem --stop-on-first-crash --use-syn-sdc --use-aroma --fs-license-file $/Applications/freesurfer/license.txt\ /Users/marloulasschuijt/Documents/BIDS/data/sub-01/Users/marloulasschuijt/Documents/BIDS/data/derivatives -w /Users/marloulasschuijt/Documents/BIDS/data/derivatives/scratch --participant_label sub-01/
Warning: <8GB of RAM is available within your Docker environment.
Some parts of fMRIPrep may fail to complete.
Continue anyway? [y/N]y
RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.09.2 -v /Users/marloulasschuijt/$/Applications/freesurfer/license.txt /Users/marloulasschuijt/Documents/BIDS/data/sub-01/Users/marloulasschuijt/Documents/BIDS/data/derivatives:/opt/freesurfer/license.txt:ro -v /Users/marloulasschuijt/sub-01:/data:ro -v /Users/marloulasschuijt:/out -v /Users/marloulasschuijt/Documents/BIDS/data/derivatives/scratch:/scratch poldracklab/fmriprep:1.3.2 /data /out participant --low-mem --stop-on-first-crash --use-syn-sdc --use-aroma --participant_label -w /scratch
usage: fmriprep [-h] [–version] [–skip_bids_validation]
[–participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL …]]
[-t TASK_ID] [–echo-idx ECHO_IDX] [–nthreads NTHREADS]
[–omp-nthreads OMP_NTHREADS] [–mem_mb MEM_MB] [–low-mem]
[–use-plugin USE_PLUGIN] [–anat-only] [–boilerplate]
[–ignore-aroma-denoising-errors] [–error-on-aroma-warnings]
[-v] [–debug]
[–ignore {fieldmaps,slicetiming,sbref} [{fieldmaps,slicetiming,sbref} …]]
[–longitudinal] [–t2s-coreg] [–bold2t1w-dof {6,9,12}]
[–output-space {T1w,template,fsnative,fsaverage,fsaverage6,fsaverage5} [{T1w,template,fsnative,fsaverage,fsaverage6,fsaverage5} …]]
[–force-bbr] [–force-no-bbr]
[–template {MNI152NLin2009cAsym}]
[–output-grid-reference OUTPUT_GRID_REFERENCE]
[–template-resampling-grid TEMPLATE_RESAMPLING_GRID]
[–medial-surface-nan] [–use-aroma]
[–aroma-melodic-dimensionality AROMA_MELODIC_DIMENSIONALITY]
[–skull-strip-template {OASIS30ANTs,NKI,MNI152NLin2009cAsym}]
[–skull-strip-fixed-seed] [–fmap-bspline] [–fmap-no-demean]
[–use-syn-sdc] [–force-syn] [–fs-license-file PATH]
[–no-submm-recon] [–cifti-output | --fs-no-reconall]
[-w WORK_DIR] [–resource-monitor] [–reports-only]
[–run-uuid RUN_UUID] [–write-graph] [–stop-on-first-crash]
[–notrack] [–sloppy]
bids_dir output_dir {participant}
fmriprep: error: argument --participant_label/–participant-label: expected at least one argument
fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues
iMac-van-Job:~ marloulasschuijt$

can you help me out here?

Thank you so much!
Marlou

#4

Try something like:

 /Users/marloulasschuijt/.local/bin/fmriprep-docker -i poldracklab/fmriprep:1.3.2 \
    --low-mem --stop-on-first-crash --use-syn-sdc --use-aroma \
    --fs-license-file $/Applications/freesurfer/license.txt \ 
    /Users/marloulasschuijt/Documents/BIDS/data \ 
    /Users/marloulasschuijt/Documents/BIDS/data/derivatives/fmriprep-1.3.2 \
    -w /Users/marloulasschuijt/Documents/BIDS/data/derivatives/scratch \
    --participant_label 01

Changes:

  • Added docker image version
  • Added space after the license.txt file (so that it is split in two arguiments)
  • Corrected data directory (should not point to a subject)
  • Corrected participant label (it is expecting a label, not a folder)
  • Improved output directory
#6

Thank you for your help!
still get this error:

-bash: /Users/marloulasschuijt/Documents/BIDS/data/derivatives/: is a directory

It is a directory but it is supposed to be one?

#7

What is the exact command line you are trying?