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Oscar
Running the BIDS validator in Oscar
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 ${bids_directory}1. Start interactive session
If you are not already inside an interactive session please start one. Here we start an interactive job of one hour. If you are using VNC, then you are already inside an interactive session and you just need to open the terminal
interact -n 2 -t 01:00:00 -m 8g
version=v1.11.0
Indicate the bids directory. This is where
dataset_description.json
file livesbids_directory=${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-${version}.sif
The following command runs the
bids-validator
executable (via singularity) to test if a directory is BIDS compliant. The command tells singularity to launch the validator-${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}
Last modified 6mo ago