Hoffman2:Software Tools:dmriprep: Difference between revisions
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singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif dmriprep -h #will list program arguments | singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif dmriprep -h #will list program arguments | ||
singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif data/bids_root/ out/ participant -w work/ | singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif data/bids_root/ out/ participant -w work/ | ||
Use singularity shell to interact with the container's environment through a shell interface. | Use singularity shell to interact with the container's environment through a shell interface. | ||
Revision as of 17:15, 13 December 2023
dmriprep
Use singularity exec to execute a specific command within the container.
module load apptainer singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif dmriprep -h #will list program arguments singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif data/bids_root/ out/ participant -w work/
Use singularity shell to interact with the container's environment through a shell interface.
module load apptainer singularity shell --userns /u/project/CCN/apps/dmriprep/dfmriprep.sif
Comprehensive documentation on dmriprep can be found at: https://www.nipreps.org/dmriprep/usage.html#usage