FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces).

Example script slurm-fsl.sh to run fslmath on 1 node of the cpu partition using 4 cores and at most 8 GB of memory:

slurm-fsl.sh

#!/bin/bash --login
#SBATCH --job-name=fsl
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --time=0-02:00:00
#SBATCH --mem=8G
#SBATCH --partition=cpu
#SBATCH --qos=cpu
##SBATCH --account=<account>
 
test -n "$SLURM_NODELIST" || exit 1
test $SLURM_NNODES -eq 1 || exit 1
 
module load apptainer
module load fsl/6.0.7.19
 
test -n "$FSL_CONTAINER" || exit 1
 
apptainer exec "$FSL_CONTAINER" /bin/bash -lc '. "$FSLDIR/etc/fslconf/fsl.sh" && fslmaths -h'

Submission example:

sbatch slurm-fsl.sh

Command to run fsl on 1 node of the cpu partition using 4 cores and at most 16 GB of memory:

srun \
    --job-name=fsl \
    --nodes=1 \
    --ntasks-per-node=1 \
    --cpus-per-task=4 \
    --mem=16G \
    --partition=cpu \
    --qos=cpu \
    --time=0-06:00:00 \
    --x11 \
    --pty \
    bash

Command to run fsl on 1 node of the gpu partition using 4 cores, at most 16 GB of memory and 1 NVIDIA P100 GPU:

srun \
    --job-name=fsl \
    --nodes=1 \
    --ntasks-per-node=1 \
    --cpus-per-task=4 \
    --mem=16G \
    --partition=gpu \
    --qos=gpu \
    --gres=gpu:p100:1 \
    --time=0-06:00:00 \
    --pty \
    --x11 \
    bash