`fmriprep` not added to output directory name

[smeisler]

singularity run \
    -B "${PWD}" \
    -B "/users/PAS2965/smeisler/workshop/babs/templateflow/":"/SGLR/TEMPLATEFLOW_HOME" \
    --env "TEMPLATEFLOW_HOME=/SGLR/TEMPLATEFLOW_HOME" \
    -B "code/license.txt":"/SGLR/FREESURFER_HOME/license.txt" \
    --containall \
    --writable-tmpfs \
    containers/.datalad/environments/fmriprep-25-0-0/image \
        "${PWD}/inputs/data/BIDS" \
        "${PWD}/outputs" \
        participant \
        -w "${PWD}/.git/tmp/wkdir" \
        --stop-on-first-crash \
        --fs-license-file /SGLR/FREESURFER_HOME/license.txt \
        --output-spaces MNI152NLin2009cAsym:res-2 \
        --slice-time-ref start \
        --skip-bids-validation \
        -vv \
        --cifti-output 91k \
        --n_cpus $SLURM_CPUS_PER_TASK \
        --mem-mb $SLURM_MEM_PER_NODE \
        --participant-label "${subid}"

The output directory should have fmriprep after it, which makes the following config items work:

zip_foldernames:
    fmriprep: "25-0-0" # folder 'fmriprep' will be zipped into 'sub-xx_(ses-yy_)fmriprep-25-0-0.zip'
    freesurfer: "7-4-1" # folder 'freesurfer' will be zipped into 'sub-xx_(ses-yy_)freesurfer-7-4-1.zip'

Other apps, like qsiprep/qsirecon, do automatically append the app name to the output directory argument.

[smeisler]

also, freesurfer is within fmriprep, so it doesn't get zipped properly.

[tsalo]

FWIW, I'm pretty sure that QSIPrep and QSIRecon don't add the pipeline name to the output directory anymore.

[smeisler]

QSIPrep and QSIrecon did, as did XCPD