#!/bin/sh
Usage() {
    echo ""
    echo "Usage: track2mask.sh  <file> <thr>"
    echo ""
    echo "You must have FSL installed in order to run this script"
    echo ""
    exit 1
}

[ "$1" = "" ] && Usage
pollo=`${FSLDIR}/bin/remove_ext $1`
shift
thr=$1
shift
max=($(${FSLDIR}/bin/fslstats ${pollo} -r | awk '{print $2}'))
cut=$(echo $max*$thr | bc)
${FSLDIR}/bin/fslmaths ${pollo} -thr ${cut} -bin ${pollo}_mask
exit 0