added --no-histmatch option

main.sh

@@ -2,16 +2,33 @@
 	SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/"	
 	t1=$1
 	mask=$2
-	outputdir=$3
+	no_hm=0
 	if [ $# -lt 2 ]; then												
-		echo $0: "usage: "$( basename $0 )" <t1.ext> <mask.ext> [<outputdir>]"
+		echo $0: "usage: "$( basename $0 )" <t1.ext> <mask.ext> [<outputdir>] [--no-histmatch]"
 		exit -1;		    
 	fi 
+	# As long as there is at least one more argument, keep looping
+	input_3="$3"
+	while [[ $# -gt 0 ]]; do
+		key="$3"
+		case "$key" in
+			--no-histmatch)
+			no_hm=1
+			;;
+			 *)
 
+			[ -z ${input_3} ] || {	outputdir=${input_3} ; }
+			;;
+		esac
+		# Shift after checking all the cass to get the next option
+		shift
+	done
+
 	echo "t1: "${t1}
 	echo "mask: "${mask}
 	input_dir=$( dirname ${t1} )
 	[ -z ${outputdir} ] && { outputdir=${input_dir}"/segmentation" ; }
+	[ -z ${no_hm} ] && { no_hm=0 ; }
 	echo "outputdir: "${outputdir}
 
 	mkdir -p ${outputdir}
@@ -21,8 +38,12 @@
 	reference=${SCRIPT_DIR}'/data/IMAGE_0426.nii.gz'
 
 	t1_hm=${proc_dir}'/t1_hm.nii.gz'
-	singularity exec -e docker://brainlife/ants:2.2.0-1bc ImageMath 3 ${t1_hm}  HistogramMatch ${t1} ${reference}  
-
+	if [ ${no_hm} == 0 ]; then
+		echo "perfroms histogram matching on reference image"
+		singularity exec -e docker://brainlife/ants:2.2.0-1bc ImageMath 3 ${t1_hm}  HistogramMatch ${t1} ${reference}  
+	else
+		singularity exec -e docker://brainlife/ants:2.2.0-1bc  ImageMath 3  ${t1_hm} Normalize  ${t1} ${mask}  && ImageMath 3 ${t1_hm} m ${t1_hm} 100  
+	fi
 	chkcp_dir=${SCRIPT_DIR}
 
 	singularity exec -e  --nv docker://gamorosino/bl_app_dbb_disseg python  ${SCRIPT_DIR}/predict.py  ${t1_hm} ${output} ${chkcp_dir} --mask ${mask}

main_local.sh

@@ -2,11 +2,27 @@
 	SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/"	
 	t1=$1
 	mask=$2
-	outputdir=$3
+
 	if [ $# -lt 2 ]; then												
-		echo $0: "usage: "$( basename $0 )" <t1.ext> <mask.ext> [<outputdir>]"
+		echo $0: "usage: "$( basename $0 )" <t1.ext> <mask.ext> [<outputdir>] [--no-histmatch]"
 		exit -1;		    
 	fi 
+	# As long as there is at least one more argument, keep looping
+	input_3="$3"
+	while [[ $# -gt 0 ]]; do
+		key="$3"
+		case "$key" in
+			--no-histmatch)
+			no_hm=1
+			;;
+			 *)
+
+			[ -z ${input_3} ] || {	outputdir=${input_3} ; }
+			;;
+		esac
+		# Shift after checking all the cass to get the next option
+		shift
+	done
 
 	echo "t1: "${t1}
 	echo "mask: "${mask}
@@ -21,7 +37,13 @@
 	reference=${SCRIPT_DIR}'/data/IMAGE_0426.nii.gz'
 
 	t1_hm=${proc_dir}'/t1_hm.nii.gz'
-	ImageMath 3 ${t1_hm}  HistogramMatch ${t1} ${reference}  
+
+	if [ ${no_hm} == 0 ]; then
+		echo "perfroms histogram matching on reference image"
+		ImageMath 3 ${t1_hm}  HistogramMatch ${t1} ${reference}  
+	else
+		ImageMath 3  ${t1_hm} Normalize  ${t1} ${mask}  && ImageMath 3 ${t1_hm} m ${t1_hm} 100  
+	fi
 
 	chkcp_dir=${SCRIPT_DIR}