Run the Batch Job

✅ Type sbatch --export sub=CAM003 runmriqc_dev.sh

✅ Go to the Jobs tab in OOD and see if the job has started yet.

✅ If the job has not failed immediately, then a subdirectory mriqc will have been created in derivatives. Look to see if it is there.

You do not need to be in interactive mode. The sbatch command will ensure the job is run as a batch job! You can start the command from any directory, but wherever you start from, the slurm log (e.g., slurm-543618.out) will be deposited there.

Caution: Job queuing

If the job remains queued for hours, you may have picked the wrong cluster. Quit and try another cluster. Sometimes, deleting and restarting a job, even on the same cluster will work! If anything goes wrong with the running job (e.g., the mriqc directory is not generated, or the job finishes in seconds, look in the slurm log to help troubleshoot. Common problems include not finding the script, not finding the right path, or subject, a typo, etc. If you start the SLURM job from the BIDS data directory, the job log will create a BIDS validation error for the next BIDS app you run!

Note that this up-to-date containerized app should NOT encounter any BIDS validator errors. This is because it should recognize all the files in this dataset.

🟢 QA & MRIQC 1: Pr (5)