Hoffman2:Software Tools:dmriprep: Difference between revisions
Jump to navigation
Jump to search
(Created page with "===dmriprep=== 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/ Comprehensive documentation on dmriprep can be found at: https://www.nipreps.org/dmriprep/usage.html#usage") |
|||
| (3 intermediate revisions by the same user not shown) | |||
| 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 | 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/ | ||
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 | 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