--- a
+++ b/scripts/multi-scan-script
@@ -0,0 +1,106 @@
+#!/bin/bash
+
+# multi-scan-script
+#
+# @brief: Run qDESS, Cubequant, and Cones analysis on super folder (absolute path) specified as an argument
+#
+# @folder structure:
+#   |subject_scans
+#       |patient01
+#           |qdess
+#           |cubequant
+#           |cones
+#       |patient02
+#           |qdess
+#           |cubequant
+#           |cones
+#       |patient03
+#           |qdess
+#           |cubequant
+#           |cones
+#       ...
+#
+# @usage (from terminal/command line):
+#   ./multi-scan-script PATH_TO_SUPER_FOLDER
+#   eg: "./multi-scan-script Users/john/Documents/subject_scans/"
+#
+# @initialization protocol:
+#   1. run "chmod +x multi-scan-script" from the command line
+#   2. Update `WEIGHTS_DIRECTORY` field below
+#
+# @notes:
+#   - If data already exists for subject, then script does not recalculate - delete `data` folder and rerun script to redo analysis
+#
+# @author: Arjun Desai, Stanford University
+#          (c) Stanford University, 2018
+
+echo "This file is currently deprecated - if needed, please make an issue on the corresponding Github repository"
+exit 125
+
+WEIGHTS_DIRECTORY="/Users/arjundesai/Documents/stanford/research/msk_pipeline_raw/weights"
+if [ -z "$WEIGHTS_DIRECTORY" ]; then
+    echo "Please define WEIGHTS_DIRECTORY in script. Use the absolute path"
+    exit 125
+fi
+
+if [ $# -eq 1 ]
+then
+SERIES="qdess"
+else
+SERIES=$2
+fi
+
+# find relevant dicom files
+
+FILES=$(find $1 -type d -name $SERIES)
+
+cd ..
+
+for i in $FILES; do
+    DIRNAME=$(dirname $i)
+    SAVE_DIRNAME="$DIRNAME/data"
+    CUBEQUANT_DIRNAME="$DIRNAME/cubequant"
+    CONES_DIRNAME="$DIRNAME/cones"
+    TARGET_SCAN="$SAVE_DIRNAME/qdess_data/echo1.nii.gz"
+    MASK="$SAVE_DIRNAME/fc/fc.nii.gz"
+
+    CUBEQUANT_INTERREGISTERED_DATA="$SAVE_DIRNAME/cubequant_data/interregistered"
+    CUEQUANT_T1RHO="$SAVE_DIRNAME/cubequant_data/t1_rho.nii.gz"
+
+
+    CONES_INTERREGISTERED_DATA="$SAVE_DIRNAME/cones_data/interregistered"
+    CONES_T2STAR="$SAVE_DIRNAME/cones_data/t2_star.nii.gz"
+
+    echo ""
+    echo "----------Analyzing $DIRNAME---------"
+
+    # use qDESS to get femoral cartilage segmentation + 3D t2 maps
+    if [ ! -e $TARGET_SCAN ]; then
+    	dosma --d $i --s $SAVE_DIRNAME qdess --fc segment --rms --weights_dir $WEIGHTS_DIRECTORY
+    	dosma --l $SAVE_DIRNAME qdess --fc t2
+	fi
+
+	# interregister cubequant with qdess
+	if [ ! -e $CUBEQUANT_INTERREGISTERED_DATA ]; then
+		echo $CUBEQUANT_INTERREGISTERED_DATA
+    	dosma --d $CUBEQUANT_DIRNAME --s $SAVE_DIRNAME cubequant interregister --ts $TARGET_SCAN --tm $MASK
+    fi
+
+    # cubequant 3D t1rho map
+    if [ ! -e $CUEQUANT_T1RHO ]; then
+    	dosma --l $SAVE_DIRNAME cubequant t1_rho
+    fi
+
+    # interregister cones with qdess
+    if [ ! -e $CONES_INTERREGISTERED_DATA ]; then
+    	dosma --d $CONES_DIRNAME --s $SAVE_DIRNAME cones interregister --ts $TARGET_SCAN --tm $MASK
+    fi
+
+    # cones 3D t2_star map
+    if [ ! -e $CONES_T2STAR ]; then
+    	dosma --l $SAVE_DIRNAME cones t2_star
+    fi
+
+    # analyze femoral cartilage
+    python -m pipeline --l $SAVE_DIRNAME knee --fc --t2 --t2_star --t1_rho
+done