#!/bin/bash

if [ $# -ne 1 ];
then

echo "Please provide path to working directory. E.g., $0 /Your/data/folder/ds001226-download"

else

dir=$1

#delete existing text files
rm -rf $dir/QC_group.txt
rm -rf $dir/QC_list.txt

#set up the header for the QC_group.txt file
echo "Group" >> $dir/QC_group.txt
echo "0" >> $dir/QC_group.txt

#set up the QC_list.txt file including the paths to all individual eddy qc folders
#set up the QC_group.txt file using code 0 for controls and 1 for patients

for s in {1..9}
do

echo "$dir/sub-CON0$s/ses-preop/dwi/eddy_unwarped_images.qc" >> $dir/QC_list.txt

echo "0" >> $dir/QC_group.txt

done

for s in {10..11}
do

echo "$dir/sub-CON$s/ses-preop/dwi/eddy_unwarped_images.qc" >> $dir/QC_list.txt

echo "0" >> $dir/QC_group.txt


done

for p in {01,02,03,06,08,10,13,14,15,17,19}
do

echo "$dir/sub-PAT$p/ses-preop/dwi/eddy_unwarped_images.qc" >> $dir/QC_list.txt

echo "1" >> $dir/QC_group.txt

done


#delete pre-existing eddy_QC folder
rm -rf $dir/eddy_squad_QC 
rm -rf $dir/eddy_squad_QC_nogroup

#run eddy group QC
eddy_squad $dir/QC_list.txt \
           -g $dir/QC_group.txt \
           -o $dir/eddy_squad_QC \
	   -u 	

#run eddy group QC without specifying group
#eddy_squad $dir/QC_list.txt \
#           -o $dir/eddy_squad_QC_nogroup \
#           --update

fi