#!/bin/sh

#   tbss_deproject - take skeleton-space voxels back to all_FA space and then, optionally, native space
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2007 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_deproject <skeleton-space-input-image> <final-space> [-n]"
    echo ""
    echo "Final-space options:"
    echo "1: just deproject <skeleton-space-input-image> onto the space of each subject in all_FA"
    echo "2: do the above and also invert nonlinear warping, to get back to subjects' native space in FAi"
    echo "3: do the above and also pad the end slices to get back to subjects' native space in orig"
    echo ""
    echo "-n : use nearest-neighbour interpolation (instead of trilinear) to keep exact values from <skeleton-space-input-image>"
    echo ""
    exit 1
}

[ "$2" = "" ] && Usage
IN=`${FSLDIR}/bin/remove_ext $1`
SPACE=$2
if [ _$3 != _ ] ; then
    interp="--interp=nn"
fi

echo "de-projecting <skeleton-space-image> into all_FA (nonlinearly aligned) subject space"
echo "output will be ${IN}_to_all_FA"
$FSLDIR/bin/tbss_skeleton -i mean_FA -p `cat thresh.txt` mean_FA_skeleton_mask_dst $FSLDIR/data/standard/LowerCingulum_1mm all_FA ${IN}_tmp -D $IN
$FSLDIR/bin/immv ${IN}_tmp_deprojected ${IN}_to_all_FA
$FSLDIR/bin/imrm ${IN}_tmp
echo "de-projection done"

if [ $SPACE -ge 2 ] ; then

    echo "now creating inverse warp fields..."
    $FSLDIR/bin/fslsplit ${IN}_to_all_FA

    preaffine=""
    if [ -f target_to_MNI152.mat ] ; then
	$FSLDIR/bin/convert_xfm -omat MNI152_to_target.mat -inverse target_to_MNI152.mat
	preaffine="--premat=../stats/MNI152_to_target.mat"
    fi

    cd ../FAi
    list=`$FSLDIR/bin/imglob -oneperimage *_FAi.*`
    list=`$FSLDIR/bin/remove_ext $list`
    echo list of original images = $list
    target=`cat best.msf`
    echo original target = $target

    for g in $list ; do
	echo "processing ${g}:"
	nextvol=`$FSLDIR/bin/imglob -oneperimage ../stats/vol0* | awk '{print $1}'`
	warp=${g}_to_${target}_nonlinear
	if [ `$FSLDIR/bin/imtest ${warp}_inv` -eq 0 ] ; then
	    $FSLDIR/bin/invwarp -w $warp -o ${warp}_inv -r $g --rel
	fi
	$FSLDIR/bin/applywarp -i $nextvol -o ../stats/${g}_${IN} -r $g -w ${warp}_inv --rel $preaffine $interp
	$FSLDIR/bin/imrm $nextvol

	# pad end slices if required
	if [ $SPACE -ge 3 ] ; then
	    cd ../stats
	    orig=`echo ${g}_${IN} | sed 's/_FAi/_orig/g'`
	    X=`${FSLDIR}/bin/fslval ${g}_${IN} dim1`
	    Y=`${FSLDIR}/bin/fslval ${g}_${IN} dim2`
	    Z=`${FSLDIR}/bin/fslval ${g}_${IN} dim3`
	    $FSLDIR/bin/fslroi ${g}_${IN} ${orig}_tmpslice 0 $X 0 $Y 0 1
	    $FSLDIR/bin/fslmaths ${orig}_tmpslice -mul 0 ${orig}_tmpslice
	    $FSLDIR/bin/fslmerge -z $orig ${orig}_tmpslice ${g}_${IN} ${orig}_tmpslice
	    Z=`echo "$Z 2 + p" | dc -`
	    $FSLDIR/bin/fslroi $orig ${orig}_tmpslice 0 $X 0 1 0 $Z
	    $FSLDIR/bin/fslmaths ${orig}_tmpslice -mul 0 ${orig}_tmpslice
	    $FSLDIR/bin/fslmerge -y $orig ${orig}_tmpslice $orig ${orig}_tmpslice
	    Y=`echo "$Y 2 + p" | dc -`
	    $FSLDIR/bin/fslroi $orig ${orig}_tmpslice 0 1 0 $Y 0 $Z
	    $FSLDIR/bin/fslmaths ${orig}_tmpslice -mul 0 ${orig}_tmpslice
	    $FSLDIR/bin/fslmerge -x $orig ${orig}_tmpslice $orig ${orig}_tmpslice
	    $FSLDIR/bin/imrm ${orig}_tmpslice
	    cd ../FAi
	fi
    done    

fi

exit 0

