Hoffman2:Software Tools:dmriprep: Difference between revisions
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Use singularity exec to execute a specific command within the container. | Use singularity exec to execute a specific command within the container. | ||
module load apptainer | module load apptainer | ||
singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif dmriprep -h | singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif dmriprep -h | ||
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/ | ||
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module load apptainer | module load apptainer | ||
singularity shell --userns /u/project/CCN/apps/dmriprep/dfmriprep.sif | singularity shell --userns /u/project/CCN/apps/dmriprep/dfmriprep.sif | ||
dmriprep -h | |||
Comprehensive documentation on dmriprep can be found at: https://www.nipreps.org/dmriprep/usage.html#usage | Comprehensive documentation on dmriprep can be found at: https://www.nipreps.org/dmriprep/usage.html#usage | ||
Latest revision as of 17:18, 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 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 dmriprep -h
Comprehensive documentation on dmriprep can be found at: https://www.nipreps.org/dmriprep/usage.html#usage