Hoffman2:Software Tools:dmriprep: Difference between revisions
Jump to navigation
Jump to search
| Line 1: | Line 1: | ||
===dmriprep=== | ===dmriprep=== | ||
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 #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 | singularity exec /u/project/CCN/apps/dmriprep/dfmriprep.sif data/bids_root/ out/ participant -w work/ | ||
or | |||
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 | Comprehensive documentation on dmriprep can be found at: https://www.nipreps.org/dmriprep/usage.html#usage | ||
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/
or
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