#!/usr/local/bin/bash
# preprocessing for DTI images acquired at FMRIB 

Usage() {
echo "REMOVE_VOLS - Remove dodgy volumes from DTI data acquired at FMRIB "
echo ""
echo "USAGE: remove_vols <input_file> <output_file> <dodgyvols> "
echo ""
echo "example: remove_vols data data_rv 4 19 35"
echo ""
echo "Note that the first volume is 0 and not 1"
echo ""
exit
}

[ "$1" = "" ] && Usage
[ "$2" = "" ] && Usage
[ "$3" = "" ] && Usage

input_file=$1
output_file=$2
current_dir=`pwd`

if [ ! -e $input_file.hdr ]; then
    echo Cant find $input_file
    exit
fi

if [ ! -e bvals ]; then
    echo Cant find bvals
    exit
fi

if [ ! -e bvecs ]; then
    echo Cant find bvecs
    exit
fi

avwsplit $input_file.hdr

vol=0
num_vols=`expr $# - 2`
t=""
rm dodgy_vols -f
echo -n $t >dodgy_vols

while [ $vol -lt $num_vols ]; do
    echo -n $t>tmp1
    echo -n $t>tmp2

    v=$3
    shift
    
    if [ -e vol000${v}.hdr ]; then
	rm vol000${v}.hdr -f
	rm vol000${v}.img -f
    fi

    if [ -e vol00${v}.hdr ]; then
	rm vol00${v}.hdr -f
	rm vol00${v}.img -f
    fi
    
    echo $v > tmp1
    cat dodgy_vols tmp1 > tmp2
    cat tmp2 > dodgy_vols

    vol=`expr $vol + 1`
done

echo "addpath('/usr/people/dtiuser/etc/FMRIB_bvals_bvecs/')">tmp3
echo "remove_vols('$current_dir')">tmp4
cat tmp3 tmp4 >tmp.m
cat tmp.m | matlab
rm tmp* -f

echo "Merging Volumes"
avwmerge -t $output_file vol*.hdr
rm vol* -f
rm dodgy_vols -f