Biowulf High Performance Computing at the NIH
MRIQC on Biowulf

MRIQC (MRI quality control) is an application that automatically extracts image quality metrics from MRI scans and generates individual reports. MRIQC can fit a classifier to categorize datasets into "accept" or "exclude" categories.

Web site

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load mriqc

[user@cn3144 ~]$ mriqc -h

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. mriqc_job.sh). For example:

#!/bin/bash

export TMPDIR=/lscratch/$SLURM_JOB_ID

module load mriqc
mriqc ds001/ MRIqc.out.ds001/ participant --participant_label sub-01 -w MRIqc.work.ds001/

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] mriqc_job.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. mriqc_jobs.swarm). For example:

mriqc ds001/ MRIqc.out.ds001/ participant --participant_label sub-01 -w MRIqc.work.ds001/
mriqc ds001/ MRIqc.out.ds001/ participant --participant_label sub-02 -w MRIqc.work.ds001/
mriqc ds001/ MRIqc.out.ds001/ participant --participant_label sub-03 -w MRIqc.work.ds001/

Submit this job using the swarm command.

swarm -f mriqc_jobs.swarm [-g #] [-t #] --module mriqc
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module mriqc Loads the mriqc module for each subjob in the swarm