--- a
+++ b/scripts/runtime-script
@@ -0,0 +1,65 @@
+#!/bin/bash
+
+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
+    echo "qDESS T2map time:"
+    python -m pipeline -d $i -s $SAVE_DIRNAME qdess -fc -t2
+
+   	echo "segmentation time:"
+    python -m pipeline -l $SAVE_DIRNAME -s $SAVE_DIRNAME qdess -fc segment -rms --weights_dir $WEIGHTS_DIRECTORY
+
+    echo "cubequant registration time:"
+	echo $CUBEQUANT_INTERREGISTERED_DATA
+    python -m pipeline -d $CUBEQUANT_DIRNAME -s $SAVE_DIRNAME cq interregister -ts $TARGET_SCAN
+
+    echo "cubequant T2map time:"
+    python -m pipeline -l $SAVE_DIRNAME cq -t1rho -fm $MASK
+
+    echo "cones registration time:"
+    python -m pipeline -d $CONES_DIRNAME -s $SAVE_DIRNAME cones interregister -ts $TARGET_SCAN
+
+    echo "cones t2star time:"
+    python -m pipeline -l $SAVE_DIRNAME cones -t2star -fm $MASK
+
+    echo "analysis time"
+    python -m pipeline -l $SAVE_DIRNAME knee -fc -t2 -t1_rho -t2_star
+done