Run the Batch Job

✅ Make sure you are in the directory where you want the SLURM logs to end up.

✅ Type:

Note

The batch job number is used to track information about the job. You can find it in the Audit tab on the HPC Portal.

✅ 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 qsirecon will have been created in derivatives and qsirecon_work will have been created in the MRIS directory.. Look to see if they are 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 will be deposited there. It should have a name similar to this slurm-543618.out. If anything goes wrong (e.g., the qsirecon 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.

Note

● qsirecon should take just over 2 hours to run the pyafq_tractometry reconstruction, and about 1.3 GB of space for the derivatives of one participant. Depending on the reconstruction qsirecon may take considerably more space than this, for example, mrtrix_multishell_msmt_ACT-hsvs reconstruction requires 17 GB of space for the derivatives of one participant!

● If it times out, you can restart it with the exact same command and the job will pick up where it left off (i.e., it'll use the work directory contents so as not to repeat any processing that was already completed).

● The qsirecon_work directory should be about 1.3 GB for the selected pyafq_tractometry reconstruction. Again, a different reconstruction choice can result in a much larger work directory: mrtrix_multishell_msmt_ACT-hsvs reconstruction requires ~25 GB for our participant. It is also possible to create custom pipelines.

🟢 dMRI: Practice 2 (~30-minutes + 2 hours job time)