Oscar

Running the BIDS validator on Oscar

0. Summary of commands

version=v1.14.14
bids_directory=${HOME}/xnat-exports/bnc/study-demodat/bids
simg=/oscar/data/bnc/simgs/bids/validator-${version}.sif
singularity exec --bind ${bids_directory}:${bids_directory}:ro ${simg} \bids-validator ${bids_directory}

1. Log into oscar and start an interactive section

If you are using the Desktop app on Open OnDemand, then you are already inside an interactive session and you just need to open the terminal. Otherwise, you can start an interactive job of 1 hour with

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

2. Define variables

Specify the version of the validator you want to use.

version=v1.14.14

You can run ls /oscar/data/bnc/simgs/bids/validator* to print all available versions

Set up paths

Specify your 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=/oscar/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}