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

To run an interactive work session, you need to connect to the gui.hpc.unipr.it server via RDP (Remote Desktop Protocol), change your keyboard layout (if necessary), open a terminal window. The following commands must be run in the terminal window.

To work in Group mode, run the newgrp command.

Example:

[foo@ui03 ~]$ groups
Person G_BAR
[foo@ui03 ~]$ newgrp G_BAR

In case you want to work in the $GROUP directory:

(G_BAR)[foo@ui03 ~]$ echo $GROUP
/hpc/group/G_BAR
(G_BAR)[foo@ui03 ~]$ cd $GROUP
(G_BAR)[foo@ui03 G_BAR]$ ...

In case you want to work in the $ARCHIVE directory:

(G_BAR)[foo@ui03 ~]$ echo $ARCHIVE
/hpc/archive/G_BAR
(G_BAR)[foo@ui03 ~]$ cd $ARCHIVE
(G_BAR)[foo@ui03 G_BAR]$ ...

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

Once you have access to the compute node, run these commands:

module load apptainer fsl
fsl.sh
fsleyes

Example:

[foo@wn82 ~]$ module load apptainer fsl
[foo@wn82 ~]$ fsl.sh 
(fsl-6.0.7.19.sif)[foo@wn82 ~]$ fsleyes

To close your work session, run the exit command twice. The first command exits the calcoloscientifico:userguide:apptainer container, while the second exits the remote node.

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

Once you have access to the compute node, run these commands:

module load apptainer fsl
fsl.sh
fsleyes

Example:

[foo@wn41 ~]$ module load apptainer fsl
[foo@wn41 ~]$ fsl.sh 
(fsl-6.0.7.19.sif)[foo@wn41 ~]$ fsleyes

To close your work session, run the exit command twice. The first command exits the calcoloscientifico:userguide:apptainer container, while the second exits the remote node.