QSIRecon template_name set to None

Software Support
24

Certainly. Here is the script I submitted to SLURM:

#!/bin/sh
apptainer run --no-mount hostfs --cleanenv --containall \
    -B /cbica/home/salot \
    -B /cbica/home/salot/qsirecon-debug/qsirecon/qsirecon:/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon \
    /cbica/home/salot/apptainer/qsirecon_unstable.sif \
    /cbica/home/salot/qsirecon-debug/derivatives/qsiprep \
    /cbica/home/salot/qsirecon-debug/derivatives/qsirecon \
    participant \
    --fs-license-file /cbica/home/salot/tokens/freesurfer_license.txt \
    --nprocs 2 \
    --participant-label sub-RM \
    -w /cbica/home/salot/qsirecon-debug/work \
    --recon-spec hbcd_scalar_maps \
    --fs-subjects-dir /cbica/home/salot/qsirecon-debug/derivatives/freesurfer \
    --output-resolution 1.7 \
    --debug all \
    -vvv

By the way, the ODF plotting step fails with that command, so I’d recommend adding --writable-tmpfs to the apptainer/Singularity call.