spm_job.sh

#!/bin/bash
#--------------------------------------------------------------
# Inputs:
#	* SUB = defined in subject_list.txt
#	* SCRIPT = MATLAB script to create and execute batch job
#	* Edit SPM path
#
# Outputs:
#	* Creates a batch job for $SUB
#	* Batch jobs are saved to the path defined in MATLAB script
#	* Executes batch job
#
# D.Cos 2017.3.7
#--------------------------------------------------------------
echo $REPLACESID $SCRIPT $SUB
if [[ -z $1 || -z $2 || -z $3 ]]; then
	if [[ -z $REPLACESID || -z $SCRIPT || -z $SUB ]]; then
		echo "Aguments not supplied on command line or in environment"
		exit 1
	fi
else
	# define subject id to replace in script from input 1
	REPLACESID=$1

	# define matlab script to run from input 2
	SCRIPT=$2

	# define subject ID from input 3
	SUB=$3
fi

# MATLAB version
MATLABVER=R2015b
SINGLECOREMATLAB=true
ADDITIONALOPTIONS=""

if "$SINGLECOREMATLAB"; then
	ADDITIONALOPTIONS="-singleCompThread"
fi

if [ "${PROCESS}" == "slurm" ]; then
	module load matlab
	MATLABCOMMAND=matlab
else
	MATLABCOMMAND="/Applications/MATLAB_"${MATLABVER}".app/bin/matlab"
fi

# create and execute job
echo -------------------------------------------------------------------------------
echo "${SUB}"
echo "Running ${SCRIPT}"
echo -------------------------------------------------------------------------------

$MATLABCOMMAND -nosplash -nodisplay -nodesktop ${ADDITIONALOPTIONS} -r "clear; addpath('$SPM_PATH'); spm_jobman('initcfg'); sub='$SUB'; script_file='$SCRIPT'; replacesid='$REPLACESID'; run('make_sid_matlabbatch.m'); spm_jobman('run',matlabbatch); exit"