Fmriprep: Error on --output-space

[wangboc]

Hi, friend:

When I type the following command, error occurs:

_fmriprep-docker --output-space T1w template --use-syn-sdc --fs-license-file /root/projects/freesurfer/license.txt /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/fmriprep/input/ /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/fmriprep/output/ participant_

Here comes the log:
RUNNING: docker run --rm -it -v /root/projects/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/ADNI/130_S_6072/Axial_fcMRI__EYES_OPEN_/2017-08-25_14_34_51.0/S601336/T1w:/data:ro -v /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/ADNI/130_S_6072/Axial_fcMRI__EYES_OPEN_/2017-08-25_14_34_51.0/S601336/template:/out poldracklab/fmriprep:1.1.1 /data /out participant --output-space --use-syn-sdc /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/fmriprep/input/ /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/fmriprep/output/ participant

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]
[--aroma-melodic-dimensionality AROMA_MELODIC_DIMENSIONALITY]
[--skull-strip-template {OASIS,NKI}] [--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]
bids_dir output_dir {participant}
fmriprep: error: argument --output-space: expected at least one argument

[chrisgorgo]

Ooops - this looks like a bug in the fmriprep-docker wrapper. While we work on fixing it please try using docker directly

docker run --rm -it -v /root/projects/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/ADNI/130_S_6072/Axial_fcMRI__EYES_OPEN_/2017-08-25_14_34_51.0/S601336/T1w:/data:ro -v /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/ADNI/130_S_6072/Axial_fcMRI__EYES_OPEN_/2017-08-25_14_34_51.0/S601336/template:/out poldracklab/fmriprep:1.1.1 /data /out participant --output-space T1w template --use-syn-sdc /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/fmriprep/input/ /root/projects/Sample/ADNI3/5.AD/ADNI3_130_S_6072/sub-ADNI3130S6072/fmriprep/output/ participant

[effigies]

I think it's an ordering thing. If I move --output-space T1w template to the end, I see the arguments show up.

Not that it isn't a bug, but I think there's a very easy workaround.