Oscar

Running the BIDS validator in Oscar

0. Summary of commands

interact -n 2 -t 01:00:00 -m 8g
version=v1.11.0
bids_directory=${HOME}/xnat-exports/bnc/study-demodat/bids
simg=/gpfs/data/bnc/simgs/bids/validator-${version}.sif
singularity exec --bind ${bids_directory}:${bids_directory}:ro ${simg} \bids-validator ${bids_directory}1. Start interactive session

If you are not already inside an interactive session please start one. Here we start an interactive job of one hour. If you are using VNC, then you are already inside an interactive session and you just need to open the terminal

1. Log into oscar and start an interactive section by typing

interact -n 2 -t 01:00:00 -m 8g

2. Define variables

Specify the version of validator to

version=v1.11.0

Set up paths

Indicate the bids directory. This is where dataset_description.json file lives

bids_directory=${HOME}/xnat-exports/bnc/study-demodat/bids

Path to Singularity Image for the bids-validator (maintained by bnc)

simg=/gpfs/data/bnc/simgs/bids/validator-${version}.sif

3. Run the main executable via singularity

The following command runs the bids-validator executable (via singularity) to test if a directory is BIDS compliant. The command tells singularity to launch the validator-${version}.sif image and execute the bids-validator command. The bids validator expects a directory as an input, which in this case corresponds to ${bids_directory}. The --bind ${bids_directory}:${bids_directory}:ro makes the ${HOME}/xnat-exports/bnc/study-demodat/bids available read-only inside the container at the same path.

singularity exec --bind ${bids_directory}:${bids_directory}:ro ${simg} \bids-validator ${bids_directory}