noMoco.sh

#!/bin/bash 
#SBATCH --job-name=SlidingWindow1       # Job name 
#SBATCH --output=monalisa_%j.out      # Standard output 
#SBATCH --error=monalisa_%j.err       # Standard error 
#SBATCH --nodes=1 
#SBATCH --ntasks=1                     # Single task 
#SBATCH --cpus-per-task=20             # Number of CPU cores 
#SBATCH --mem=100G                     # Memory 
#SBATCH --time=10:00:00                # Walltime 
#SBATCH --nodelist=chacha              # Optional: force node 
echo "Job ID: $SLURM_JOB_ID"  
# Build MATLAB command string 
MATLAB_CMD="addpath(genpath('/usr/src/app')); compile_mex_for_monalisa; run('/usr/src/app/scripts/Mathilda_NoMoco_Recon.m'); exit;" 
# Run Apptainer + MATLAB in one go 
apptainer exec \
  --bind /home/yannic.delisle/mnt/yannic.delisle:/usr/src/app/Data \
  --bind /home/yannic.delisle/mnt/yannic.delisle/pulseq:/usr/src/app/pulseq \
  --bind /home/yannic.delisle/mnt/yannic.delisle/monalisa_tutorial_ui:/usr/src/app/monalisa_tutorial_ui \
  --bind /home/yannic.delisle/mnt/yannic.delisle/mapVBVD:/usr/src/app/mapVBVD \
  --bind /home/yannic.delisle/mnt/yannic.delisle/scripts:/usr/src/app/scripts \
  --bind /home/yannic.delisle/mnt/yannic.delisle/rigid_motion_correction_monalisa_spm:/usr/src/app/rigid_motion_correction_monalisa_spm \
  --bind /home/yannic.delisle/mnt/yannic.delisle/spm:/usr/src/app/spm \
  --writable-tmpfs \
  --env MLM_LICENSE_FILE=27000@matlablm.hevs.ch \
  /home/yannic.delisle/app/monalisa.sif \
  bash -c "chmod -R ugo+x /usr/src/app/scripts && matlab -nodisplay -nosplash -r \"${MATLAB_CMD}\""