--- a
+++ b/scripts/bilateral-knee-dess
@@ -0,0 +1,123 @@
+#!/bin/bash
+
+# 1. Separate dicom files from bilateral dess knee scan into left dicoms and right dicoms
+# 2. Run qDESS analysis on left and right knees
+#
+# @usage (from terminal/command line):
+# ./bilateral-knee-dess PATH_TO_DICOM_FOLDER PATIENT_ID
+# eg: "./bilateral-knee-dess /Users/data/Patient07/005 07"
+#
+# @initialization protocol:
+#   1. run "chmod +x bilateral-knee-dess" from the command line
+#   2. Update `WEIGHTS_DIRECTORY` field below to point to the appropriate weights
+#   3. Update 'TISSUES' field if additional tissues desired
+#      e.g. '--fc --tc' for femoral cartilage and tibial cartilage
+#
+# @assumptions:
+#   - Scan volumes are acquired in sagittal direction from patient left to patient right
+#     (i.e. left knee, then right knee)
+#   - Volume slices (1...N) - Left knee slices (1...N/2), right knee slices (N/2 + 1, ... N)
+#   - Left knee - lateral --> medial
+#   - Right knee - medial --> lateral
+#
+# @author: Arjun Desai, Stanford University
+#          (c) Stanford University, 2018
+
+
+SCRIPTS_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+DOSMA_DIR="$( cd "$( dirname "${SCRIPTS_DIR}" )" >/dev/null 2>&1 && pwd )"
+
+WEIGHTS_DIRECTORY=$DOSMA_DIR/"../weights"
+TISSUES='--fc'
+
+if [[ -z "$WEIGHTS_DIRECTORY" ]]; then
+    echo "Please define WEIGHTS_DIRECTORY in script. Use the absolute path"
+    exit 125
+fi
+
+if [[ $# -lt 1 ]]; then
+	echo "Please provide path to dicom folder and patient id"
+	exit 125
+fi
+
+if [[ $# -lt 2 ]]; then
+	echo "Please provide patient id"
+	exit 125
+fi
+
+DICOM_PATH=$1
+PID=$2
+echo "dicom path: $DICOM_PATH"
+echo "patient id: $PID"
+
+# get list of dicoms in this folder
+dicom_list_str=$(find $DICOM_PATH -type f -name "*.dcm" -maxdepth 1 | sort)
+dicom_array=()
+for filepath in $dicom_list_str
+do
+    dicom_array+=($filepath)
+done
+
+echo "Number of dicoms: ${#dicom_array[@]}"
+
+# halfpoint in dicom list to split 
+half_point=$((${#dicom_array[@]} / 2))
+
+# Assume directories exist, if they don't set this to false
+DIRS_EXIST=1
+
+LEFT_DIR="$DICOM_PATH/LEFT/"
+if [[ ! -d "$LEFT_DIR" ]]; then
+	mkdir $LEFT_DIR
+	DIRS_EXIST=0
+fi
+
+RIGHT_DIR="$DICOM_PATH/RIGHT/"
+if [[ ! -d "$RIGHT_DIR" ]]; then
+	mkdir $RIGHT_DIR
+    DIRS_EXIST=0
+fi
+
+# if the directories already exist, assume the data has already been separated into different folders
+if [[ $DIRS_EXIST -eq 0 ]]; then
+    counter=1
+    for filepath in ${dicom_array[@]}
+    do
+
+        filename=$(basename $filepath)
+
+        if [[ $counter -gt $half_point ]]; then
+            # store in right directory
+            cp $filepath $RIGHT_DIR
+        else
+            cp $filepath $LEFT_DIR
+        fi
+
+        counter=$(expr $counter + 1)
+    done
+fi
+
+cd ..
+
+base_dicom_path=$(dirname $DICOM_PATH)
+base_filename=$(basename $DICOM_PATH)
+DATA_DIR="$base_dicom_path/data/$base_filename"
+
+echo "Save path: $DATA_DIR"
+
+# 2. run analysis on the qdess files
+#    if data directory already exist, skip analysis
+
+DATA_DIR_LEFT="$DATA_DIR/LEFT"
+
+dosma --d $LEFT_DIR --s $DATA_DIR_LEFT qdess $TISSUES segment --rms --weights_dir $WEIGHTS_DIRECTORY
+dosma --l $DATA_DIR_LEFT qdess $TISSUES t2
+dosma --l $DATA_DIR_LEFT knee --pid $PID $TISSUES
+
+
+DATA_DIR_RIGHT="$DATA_DIR/RIGHT"
+
+dosma --d $RIGHT_DIR --s $DATA_DIR_RIGHT qdess $TISSUES segment --rms --weights_dir $WEIGHTS_DIRECTORY
+dosma --l $DATA_DIR_RIGHT qdess $TISSUES t2
+dosma --l $DATA_DIR_RIGHT knee --ml --pid $PID $TISSUES
+