#!/bin/bash

# To give your job a name
#SBATCH --job-name=FS1

# To receive an email when job completes or fails
#SBATCH --mail-user=luigisaccaro@gmail.com
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL

# Request CPU resource for a serial job
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1

# Memory usage (MB)
#SBATCH --mem-per-cpu=32000

# Set your minimum acceptable walltime, format: day-hours:minutes:seconds
#SBATCH --time=20:00:00

# Set the file for output (stdout)
# SBATCH --output="${OUTPUT_DIR}/${INPUTFILE}_run_output.txt"

# Set the file for error log (stderr)
# SBATCH --error="${OUTPUT_DIR}/${INPUTFILE}_run_error.txt"

# Set the working directory

#SBATCH --chdir=/home/users/s/saccaro/

# SBATCH --workdir=/home/users/s/saccaro/

# write you bash command below

# setup FS, after putting SetUpFreeSurfer.sh in the directory

module load FreeSurfer/6.0.0-centos6_x86_64

source /home/users/s/saccaro/SetUpFreeSurfer.sh

# create directory

FSDIR="/home/users/s/saccaro/Groupe_0"

mksubjdris ${FSDIR}/S001;

mri_convert -i ${FSDIR}/S001/scans/struct/s44891-153636-00001-00192-1.nii -o ${FSDIR}/S001/scans/struct/s44891-153636-00001-00192-1.mgz

recon-all -all -s S001