Chapter 4 MRIQC
On the remote computer make output directory.
mkdir -p /work/ashley.ware/data/ACAP/mriqc
4.1 Job Script
Create job script.
vi ~/scripts/ACAP/mriqc-job.sh
Copy and paste.
#!/bin/bash
#SBATCH --time=10:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=16G # memory per CPU core
# LOAD ENVIRONMENTAL VARIABLES
username=`id -un`
# INSERT CODE, AND RUN YOUR PROGRAMS HERE
echo ${1} ${2}
singularity run \
--bind /work/${username}/BIDS/ACAP:/data:ro \
--bind /work/${username}/data/ACAP/mriqc:/out \
/home/${username}/apps/mriqc.img \
/data \
/out \
participant \
--participant_label ${1} \
--session-id ${2} \
-m T1w \
--no-sub
4.2 Batch Script
First check that your subjid
and ses
are correct.
for i in $(find /work/ashley.ware/BIDS/ACAP/ -name "*T1w.nii"); do
subjid=`echo $i | cut -d "/" -f6`
ses=`echo $i | cut -d "/" -f7`
echo $subjid
done
If everything is correct then you can create your batch file.
Create batch script.
vi ~/scripts/ACAP/mriqc-batch.sh
Copy and paste.
#!/bin/bash
curTime=`date +"%Y%m%d-%H%M%S"`
username=`id -un`
mkdir -p ~/logfiles/ACAP/${curTime}
for i in $(find /work/${username}/BIDS/ACAP/ -name "*T1w.nii"); do
subjid=`echo $i | cut -d "/" -f6`
ses=`echo $i | cut -d "/" -f7`
sbatch \
-o ~/logfiles/ACAP/${curTime}/output-${subjid}_${ses}.txt \
-e ~/logfiles/ACAP/${curTime}/error-${subjid}_${ses}.txt \
~/scripts/ACAP/mriqc-job.sh \
${subjid:4} \
${ses:4}
sleep 1
done
4.3 Submit Jobs with Batch Script
Submit jobs.
sh ~/scripts/ACAP/mriqc-batch.sh
You can check the status of your jobs by checking if it is running or pending.
squeue
You can check the outputs.
tail -n 5 ~/logfiles/ACAP/<date>/output*
4.4 Download Directory / Sync Directory with Arc
Back on your local computer make sure you have the directory already.
mkdir -p /Volumes/bobo/data/ACAP/mriqc
Then sync the data from the remote computer to your local computer.
rsync -rauv \
ashley.ware@arc.ucalgary.ca:/work/ashley.ware/data/ACAP/mriqc/ \
/Volumes/bobo/data/ACAP/mriqc/