eddy_correct

#!/bin/sh

#   Copyright (C) 2004-8 University of Oxford
#
#   SHCOPYRIGHT

Usage() {
    echo ""
    echo "Usage: eddy_correct <4dinput> <4doutput> <reference_no>"
    echo ""
    exit
}

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

input=`${FSLDIR}/bin/remove_ext ${1}`
output=`${FSLDIR}/bin/remove_ext ${2}`
ref=${3}

if [ `${FSLDIR}/bin/imtest $input` -eq 0 ];then
    echo "Input does not exist or is not in a supported format"
    exit
fi

fslroi $input ${output}_ref $ref 1

fslsplit $input ${output}_tmp
full_list=`${FSLDIR}/bin/imglob ${output}_tmp????.*`

for i in $full_list ; do
    echo processing $i
    echo processing $i >> ${output}.ecclog
    ${FSLDIR}/bin/flirt -in $i -ref ${output}_ref -nosearch -o $i -paddingsize 1 >> ${output}.ecclog
done

fslmerge -t $output $full_list

/bin/rm ${output}_tmp????.* ${output}_ref*