#!/bin/sh

#   tbss_3_postreg - post-registration processing
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2005-2008 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
#   
#   
#   LICENCE
#   
#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
#   Oxford (the "Software")
#   
#   The Software remains the property of the University of Oxford ("the
#   University").
#   
#   The Software is distributed "AS IS" under this Licence solely for
#   non-commercial use in the hope that it will be useful, but in order
#   that the University as a charitable foundation protects its assets for
#   the benefit of its educational and research purposes, the University
#   makes clear that no condition is made or to be implied, nor is any
#   warranty given or to be implied, as to the accuracy of the Software,
#   or that it will be suitable for any particular purpose or for use
#   under any specific conditions. Furthermore, the University disclaims
#   all responsibility for the use which is made of the Software. It
#   further disclaims any liability for the outcomes arising from using
#   the Software.
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#   innovation@isis.ox.ac.uk quoting reference DE/9564.
export LC_ALL=C

Usage() {
    cat <<EOF

Usage: tbss_3_postreg [options]

Choose ONE of:
 -S   : derive mean_FA and mean_FA_skeleton from mean of all subjects in study (recommended)
 -T   : use FMRIB58_FA and its skeleton instead of study-derived mean and skeleton

EOF
    exit 1
}

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

if [ $1 = -S ] ; then
    SKELETON=0
elif [ $1 = -T ] ; then
    SKELETON=1
else
    Usage
fi

echo [`date`] [`hostname`] [`uname -a`] [`pwd`] [$0 $@] >> .tbsslog

cd FA

/bin/rm -f all.msf

if [ `${FSLDIR}/bin/imtest target` = 1 ] ; then
    echo "using pre-chosen target for registration"
    best=target
else
    echo "finding best target"

    n=`$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr* | wc -w`

    for f in `$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*` ; do

	meanscore=0
	medianscore=0

	for g in `$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*` ; do
	
	    thismeanscore=`cat ${g}_to_${f}_warp.msf | awk '{print $1}'`
	    thismedianscore=`cat ${g}_to_${f}_warp.msf | awk '{print $2}'`

	    meanscore=`echo "10 k $meanscore $thismeanscore + p" | dc -`
	    medianscore=`echo "10 k $medianscore $thismedianscore + p" | dc -`
	done

	meanscore=`echo "10 k $meanscore $n / p" | dc -`
	medianscore=`echo "10 k $medianscore $n / p" | dc -`

	echo "$f $meanscore $medianscore"
	echo "$f $meanscore $medianscore" >> all.msf

    done

    best=`cat all.msf | sort -k 2 -n | head -n 1 | awk '{print $1}'`
    echo "best target is $best - now registering this to standard space"

    $FSLDIR/bin/imcp $best target
fi

echo $best > best.msf

mkdir -p ../stats

# is target already in MNI152 space? (kludge)
if [ `${FSLDIR}/bin/imtest target` = 1 ] && [ `$FSLDIR/bin/fslval $best dim1` = 182 ] && [ `$FSLDIR/bin/fslval $best dim2` = 218 ] && [ `$FSLDIR/bin/fslval $best dim3` = 182 ] ; then

    echo "transforming all FA images into MNI152 space"
    filelist=`$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*`;
    # check that all the registration results are there!
    missingwarps="";
    for f in $filelist ; do
	if [ `${FSLDIR}/bin/imtest ${f}_to_target_warp` = 0 ] ; then
	    missingwarps="$missingwarps ${f}_to_target_warp"
	fi
    done
    if [ `echo $missingwarps | wc -c` -gt 1 ] ; then
	echo "ERROR:: cannot find the following warp results:"
	echo "    $missingwarps"
	echo "Please wait for registration (fnirt) to finish or re-run registrations";
	exit 1;
    fi
    for f in $filelist ; do
	echo $f
	$FSLDIR/bin/applywarp -i $f -o ${f}_to_target -r target -w ${f}_to_target_warp --rel
    done

else

    echo "affine-registering target to MNI152 space"
    $FSLDIR/bin/fslmaths target -bin target_mask
    $FSLDIR/bin/flirt -in target -inweight target_mask -ref $FSLDIR/data/standard/FMRIB58_FA_1mm -omat target_to_MNI152.mat -out target_to_MNI152

    echo "transforming (and upsampling) all FA images into MNI152 space"
    for f in `$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*` ; do
	echo $f
	$FSLDIR/bin/applywarp -i $f -o ${f}_to_target -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w ${f}_to_${best}_warp --postmat=target_to_MNI152.mat
    done

fi

echo "merging all upsampled FA images into single 4D image"
${FSLDIR}/bin/fslmerge -t ../stats/all_FA `$FSLDIR/bin/imglob *_FA_to_target.*`
cd ../stats

# create mean FA
echo "creating valid mask and mean FA"
$FSLDIR/bin/fslmaths all_FA -max 0 -Tmin -bin mean_FA_mask -odt char
$FSLDIR/bin/fslmaths all_FA -mas mean_FA_mask all_FA
$FSLDIR/bin/fslmaths all_FA -Tmean mean_FA

# create skeleton
if [ $SKELETON = 0 ] ; then
    echo "skeletonising mean FA"
    $FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
else
    $FSLDIR/bin/fslmaths $FSLDIR/data/standard/FMRIB58_FA_1mm -mas mean_FA_mask mean_FA
    $FSLDIR/bin/fslmaths mean_FA -bin mean_FA_mask
    $FSLDIR/bin/fslmaths all_FA -mas mean_FA_mask all_FA
    $FSLDIR/bin/imcp $FSLDIR/data/standard/FMRIB58_FA-skeleton_1mm mean_FA_skeleton
fi

echo "now view mean_FA_skeleton to check whether the default threshold of 0.2 needs changing, when running:"
echo "tbss_4_prestats <threshold>"

