Dual regression on HPC

HPC Support HPC issues
1

Hello, i am trying to do a dual regression on HPC, but it’s not working. Each time it seems to work but I don’t have any output.

Here is my code:

module load GCC/8.3.0

module load OpenMPI/3.1.4

module load FSL/6.0.3-Python-3.7.4

\# The melodic output

MELODIC_IC="/home/users/l/lemarec4/data_ICA/GroupICA_T0_T1.ica/melodic_IC.nii.gz"

\# Output directory for dual regression results

RESULTS_DIR="/home/users/l/lemarec4/Results_dualreg"

\# Must be the SAME list (same order) used for MELODIC

INPUT_LIST="/home/users/l/lemarec4/data_ICA/inputs_4_ica.txt"

\# Perform thresholded dual regression to obtain unbiased timeseries for connectomics analyses (e.g., with FSLnets)

THR_FLAG="--thr"

mkdir -p "${RESULTS_DIR}"

\# ---------------------------

\# 3) Run Dual Regression (Stages 1 & 2 only)

\# ---------------------------

\# Arguments: <groupICs> <des_norm> <design.mat> <design.con> <n_perm> <outdir> <subjects...>

\# Here: "0 -1 0" means: no group-level stage 3 here (stages 1 & 2 only)

echo "Running dual_regression on inputs from: ${INPUT_LIST}"

srun dual_regression   "${MELODIC_IC}"   0 -1 0 ${THR_FLAG}   "${RESULTS_DIR}"   \`cat "${INPUT_LIST}"\`

echo "Done. Main outputs:"

echo " - ${RESULTS_DIR}/dr_stage1/ (time courses)"

echo " - ${RESULTS_DIR}/dr_stage2_icXXXX.nii.gz (subject spatial maps per IC)"

Can you help me ?
Thank you so much !

2

Dear @Faustine.Lemarechal

Please try with the latest version, this one is very old.

ml GCC/10.3.0  OpenMPI/4.1.1 FSL/6.0.5.1

Which command do you use to start your job?

3

Hello, thank you so much for your help. But it didn’t work even with your advices. It seems that BAOBAB does not include fsl_sub which the script includes. There is my script:

#!/bin/bash

#SBATCH --time=10:00:00               # NOTE: likely longer than generally needed 

#SBATCH --ntasks 1

#SBATCH --cpus-per-task=16

#SBATCH --partition=shared-cpu

\# Outputs ----------------------------------

#SBATCH --output log/%x-%A-%a.out

#SBATCH --error log/%x-%A-%a.err

#SBATCH --mail-user=faustine.lemarech@hes-so.ch

#SBATCH --mail-type=ALL

\# ------------------------------------------



\# ---------------------------

\# USER PARAMETERS TO EDIT

\# ---------------------------

MELODIC_IC="/home/users/l/lemarec4/data_ICA/GroupICA_T0_T1.ica/melodic_IC.nii.gz"

RESULTS_DIR="/home/users/l/lemarec4/Results_dualreg"

INPUT_LIST="/home/users/l/lemarec4/data_ICA/inputs_4_ica.txt"

THR_FLAG="--thr"



\# Crée le dossier de sortie si nécessaire

mkdir -p "${RESULTS_DIR}"



\# ---------------------------

\# Load FSL (Baobab modules)

\# ---------------------------

ml purge

ml GCC/10.3.0 OpenMPI/4.1.1 FSL/6.0.5.1



\# Permet à FSL de trouver les packages Python (nibabel, etc.)

export PYTHONPATH=/home/users/l/lemarec4/.local/lib/python3.9/site-packages:$PYTHONPATH

export FSLPARALLEL=0

\# ---------------------------

\# Run Dual Regression (Stages 1 & 2 only)

\# ---------------------------

echo "Running dual_regression on inputs from: ${INPUT_LIST}"



dual_regression "${MELODIC_IC}" 0 -1 0 ${THR_FLAG} "${RESULTS_DIR}" $(cat "${INPUT_LIST}") --nobet




echo "Done. Main outputs:"

echo " - ${RESULTS_DIR}/dr_stage1/ (time courses)"

echo " - ${RESULTS_DIR}/dr_stage2_icXXXX.nii.gz (subject spatial maps per IC)"

Thank you again

4

You can load the module NiBabel/3.2.1 instead.

This is for testing? For production later, be careful to specify the number of cores you request.

I’ll install a newer version, it seems it is now installed by default.

5