#!/bin/bash

# msk-qdess

#

# @brief: Run DESS analysis for femoral cartilage on patient folder specified as an argument

#           1. Do automatic segmentation

#           2. Calculate T2 map

#           3. Analyze all supp

#

# @usage (from terminal/command line):

#   ./msk-qdess PATH_TO_PATIENT_FOLDER qDESS_DICOM_FOLDER_NAME

#   eg: "./msk-qdess subject_scans/patient01 001"

#

# @initialization protocol:

#   1. run "chmod +x msk-qdess" from the command line

#   2. Update `WEIGHTS_DIRECTORY` field below

#

# @author: Arjun Desai, Stanford University

#          (c) Stanford University, 2018

WEIGHTS_DIRECTORY=""

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)

    DIRNAME="$DIRNAME/data"

    dosma --d $i --s $DIRNAME qdess --fc segment --rms --weights_dir $WEIGHTS_DIRECTORY

    dosma --l $DIRNAME qdess --fc t2

    dosma --l $DIRNAME knee --fc --t2

done