Comment on page

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}
​

XNAT to BIDS - Previous

BIDS Validation

Docker

Last modified 6mo ago