Help running fmriprep_ciftify on singularity

Hi all,

I’m trying to run fmriprep_ciftify on an HPC that run Singularity.

Before that, on my machine, I successfully ran with the following command:

docker run -ti --rm -v $BASE/BIDS:/bids:ro -v $BASE:/out -v $FS_LICENSE_DIR:/fs-license \
tigrlab/fmriprep_ciftify:latest /bids /out participant --participant_label=JnDo --session_label=001 \
--fs-license /fs-license/license.txt --fmriprep-args="--use-aroma"

Following instructions from here, I used

docker run --privileged -t --rm \
    -v /var/run/docker.sock:/var/run/docker.sock \
    -v /absolute/path/to/output/folder:/output \
    singularityware/docker2singularity \

To create the image. Then I tried to run

singularity run --cleanenv \
    -B $ASSUTA_DIR:/data \
    -B $FS_LICENSE:/fs-license \
    $LAB_PATH/Singularity/tigrlab_fmriprep_ciftify_latest-2019-08-16-6ea864911724.simg \
    /data/BIDS /data participant  \
    --participant-label=${SUBJECTS[${SLURM_ARRAY_TASK_ID}]} \
    --session_label=001  --fs-license="/fs-license/license.txt" --fmriprep-args="--use-aroma"

And got the following error:

Usage: <bids_dir> <output_dir> <analysis_level> [options]

That’s it! I’ve look a gazillion times on the command, trying to find what has gone wrong and couldn’t.
If someone can help me with that, that would be dearly appreciated.

Hi @urielias

Not a direct answer to your question, but I’d note that that container looks to be 2+ years old, using a version of fMRIPrep that is sure to be outdated (1.3.2, most recent is 21.0.0rc2). Is there a reason you want to use this specifically, as opposed to running the latest fMRIPrep release with cifti outputs? I also don’t think you need the “=” between your named arguments.


Thanks! My preference for this tool is that it creates a full HCP-like library which makes it easier with wb_view etc. However, probably the best of all is to run fmriprep and ciftify_subject separately.