#!/bin/sh

#   tbss_fill - thicken skeleton stats results for display purposes
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2006-2008 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
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Usage() {
    echo ""
    echo "Usage: tbss_fill <stats_image> <threshold> <mean_FA> <output> [-n]"
    echo "  -n : include negative stat values (below -threshold)"
    echo ""
    exit 1
}

do_tbss_fill() {
    IN=$1
    OUT=$2

    # threshold the input then convolve with sphere of radius 3mm
    $FSLDIR/bin/fslmaths $IN -thr $THRESH -kernel sphere 3 -fmean $OUT -odt float

    # renorm so that the max is same as input's max
    $FSLDIR/bin/fslmaths $OUT -div `${FSLDIR}/bin/fslstats $OUT -p 100` -mul `${FSLDIR}/bin/fslstats $IN -p 100` $OUT

    # average with thresholded input (to enhance appearance of skeleton within final output)
    # then multiply by mean-FA (to ensure we stay within real tracts)
    $FSLDIR/bin/fslmaths $IN -thr $THRESH -add $OUT -div 2 -mul $MEANFA -div `${FSLDIR}/bin/fslstats $MEANFA -p 100` $OUT -odt float

    # final thresholding at 1/50 of max value
    $FSLDIR/bin/fslmaths $OUT -thr `${FSLDIR}/bin/fslstats $OUT -R | awk '{print "10 k " $2 " 50 / p"}' | dc -` $OUT
}

[ "$4" = "" ] && Usage

STATS=$1
THRESH=$2
MEANFA=$3
OUTPUT=$4

if [ `${FSLDIR}/bin/imtest $STATS` = 0 ] || [ `${FSLDIR}/bin/imtest $MEANFA` = 0 ] ; then
    echo "Error - either <stats_image> or <mean_FA> is not valid"
    Usage
fi

do_tbss_fill $STATS $OUTPUT

if [ "$5" != "" ] ; then
    $FSLDIR/bin/fslmaths $STATS -mul -1 ${OUTPUT}neg
    do_tbss_fill ${OUTPUT}neg ${OUTPUT}negout
    $FSLDIR/bin/fslmaths $OUTPUT -sub ${OUTPUT}negout $OUTPUT
    /bin/rm ${OUTPUT}neg*
fi

