#!/bin/sh

#   tbss_sym - make symmetric skeleton for TBSS left-right testing
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2008-2009 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
#   
#   
#   LICENCE
#   
#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
#   Oxford (the "Software")
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#   University").
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export LC_ALL=C

Usage () {
    echo ""
    echo "Usage: tbss_sym <image-rootname>"
    echo "e.g. tbss_sym FA"
    echo "e.g. tbss_sym L2"
    echo ""
    exit 1
}

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

thresh=`cat thresh.txt`
ALTIM=$1

if [ `${FSLDIR}/bin/imtest mean_FA_symmetrised_skeleton_mask_dst` -eq 0 ]; then

    echo "creating a symmetrised skeleton"
    $FSLDIR/bin/fslmaths mean_FA_skeleton -thr $thresh -bin -dilF grotsym_dilated
    $FSLDIR/bin/fslswapdim mean_FA -x y z grotsym > /dev/null
    $FSLDIR/bin/fslmaths mean_FA -mas grotsym -add grotsym -div 2 mean_FA_symmetrised
    $FSLDIR/bin/tbss_skeleton -i mean_FA_symmetrised -o grotsym_symmetrised_skeleton
    $FSLDIR/bin/fslmaths grotsym_symmetrised_skeleton -thr $thresh -mas grotsym_dilated grotsym_symmetrised_skeleton
    $FSLDIR/bin/fslswapdim grotsym_symmetrised_skeleton -x y z grotsym > /dev/null
    $FSLDIR/bin/fslmaths grotsym_symmetrised_skeleton -mas grotsym mean_FA_symmetrised_skeleton
    $FSLDIR/bin/fslmaths mean_FA_symmetrised_skeleton -bin mean_FA_symmetrised_skeleton_mask

    echo "creating symmetrised skeleton distancemap"
    ${FSLDIR}/bin/fslmaths mean_FA_mask -mul -1 -add 1 -add mean_FA_symmetrised_skeleton_mask mean_FA_symmetrised_skeleton_mask_dst
    ${FSLDIR}/bin/distancemap -i mean_FA_symmetrised_skeleton_mask_dst -o mean_FA_symmetrised_skeleton_mask_dst

fi

echo "projecting all FA data onto symmetrised skeleton"
if [ $ALTIM != "FA" ]; then
    altim="-a all_${ALTIM}"
fi
${FSLDIR}/bin/tbss_skeleton -i mean_FA_symmetrised -p $thresh mean_FA_symmetrised_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_${ALTIM}_symmetrised_skeletonised $altim -s mean_FA_symmetrised_skeleton

echo "flipping, substracting and half-masking 4D skeletonised FA"
$FSLDIR/bin/fslswapdim all_${ALTIM}_symmetrised_skeletonised -x y z grotsym_all_${ALTIM}_symmetrised_flipped > /dev/null
$FSLDIR/bin/fslmaths all_${ALTIM}_symmetrised_skeletonised -sub grotsym_all_${ALTIM}_symmetrised_flipped -roi 91 91 0 218 0 182 0 `$FSLDIR/bin/fslval all_FA_skeletonised dim4` all_${ALTIM}_skeletonised_left_minus_right

$FSLDIR/bin/imrm grotsym*

