QSIPREP configures pipelines for processing diffusion-weighted MRI (dMRI) data.

Web site

• Home page
• Github page

• QSIPREP Documentation

• Module Name: qsiprep (see the modules page for more information)

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 qsiprep

[user@cn3144 ~]$ qsiprep -h

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

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

#!/bin/bash
# sbatch --gres=lscratch:100 --mem=32g --cpus-per-task=48 --time=72:00:00 qsiprep.sh

set -e

function fail {
    echo "FAIL: $@" >&2
    exit 1  # signal failure
}

module load qsiprep
qsiprep /data/$USER/ds000114-download /data/$USER/qsiprep.out.ds001 \
participant --participant_label sub-02 -w /lscratch/$SLURM_JOB_ID \
--notrack --nthreads $SLURM_CPUS_PER_TASK --mem_mb $SLURM_MEM_PER_NODE \
--stop-on-first-crash --output-resolution 1.2

Submit this job using the Slurm sbatch command.

sbatch [--gres=lscratch:#] [--cpus-per-task=#] [--mem=#] qsiprep.sh

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

export TMPDIR=/lscratch/$SLURM_JOB_ID; \
mkdir -p $TMPDIR/out; \
mkdir -p $TMPDIR/wrk; \
qsiprep /data/$USER/ds000114-download $TMPDIR/out \
participant --participant_label sub-01 -w $TMPDIR/wrk \
--notrack --nthreads $SLURM_CPUS_PER_TASK \
--mem_mb $SLURM_MEM_PER_NODE
--stop-on-first-crash --output-resolution 1.2; \
mv $TMPDIR/out /data/$USER/QSIPREP.out.s001
export TMPDIR=/lscratch/$SLURM_JOB_ID; \
mkdir -p $TMPDIR/out; \
mkdir -p $TMPDIR/wrk; \
qsiprep /data/$USER/ds000114-download $TMPDIR/out \
participant --participant_label sub-02 -w $TMPDIR/wrk \
--notrack --nthreads $SLURM_CPUS_PER_TASK \
--mem_mb $SLURM_MEM_PER_NODE
--stop-on-first-crash --output-resolution 1.2; \
mv $TMPDIR/out /data/$USER/QSIPREP.out.s002

Submit this job using the swarm command.

swarm -f qsiprep.swarm [--gres=lscratch:#] [-g #] [-t #] --module qsiprep