submit.sh

#!/bin/bash
#
#SBATCH --job-name="connectivity_1M"
#
#SBATCH --cpus-per-task=4
#SBATCH --time=06:00:00 
#SBATCH --mem=16G
#SBATCH --mail-type='FAIL'
#SBATCH --mail-user='valentine.lahy@student.uclouvain.be'

#SBATCH --output=/auto/home/users/v/l/vlahy/logs/connectivity_1M_%A_%a.out
#SBATCH --error=/auto/home/users/v/l/vlahy/logs/connectivity_1M_%A_%a.err

# For a single subject, uncomment and replace following lines
#root_out="/globalscratch/ucl/elen/vlahy/"
#root_in="/CECI/proj/pilab/PermeableAccess/alzheimer_kDs4Eb69VO/study/"
#subject_id="TAU_95_ses-0"

root_out="$3" 
root_in="$2"
json_file="$1"

# Process JSON to extract patient list
raw_json=$(<"$json_file")
cleaned_json=$(echo "$raw_json" | sed 's/[][]//g' | tr ',' '\n' | tr -d '"' | tr -d ' ')
mapfile -t patients <<< "$cleaned_json"
subject_id=${patients[$SLURM_ARRAY_TASK_ID]}


python /auto/home/users/v/l/vlahy/code/connectivity_matrix.py \
  "$root_in" \
  "$root_out" \
  "$subject_id"
# tcksift2 "$tck" "$odf" "$weights_txt" -out_mu "$mu_txt" -force
# à modifier avec le bon script 
#python /auto/home/users/v/l/vlahy/code/all_scores_patients_vs_volontaires.py 
#python /auto/home/users/v/l/vlahy/code/all_scores_patients_vs_volontaires.py "$root_in" "$root_out" "$subject_id"
# python /auto/home/users/v/l/vlahy/code/connectivity_matrix_sift2_mrtrix.py \
#   "$root_out" \
#   "$subject_id" \
#   20