#!/bin/sh

#   tbss_2_reg - TBSS nonlinear registration
#
#   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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#   University harmless from and against any and all claims, damages and
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#   negligence) which arise directly or indirectly from the use of the
#   Software or the sale of any products based on the Software.
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#   No part of the Software may be reproduced, modified, transmitted or
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#   
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#   commercially. Use for which any financial return is received shall be
#   defined as commercial use, and includes (1) integration of all or part
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#   Innovation Limited ("Isis"), the technology transfer company of the
#   University, to negotiate a licence. Contact details are:
#   innovation@isis.ox.ac.uk quoting reference DE/9564.

Usage() {
    cat <<EOF

Usage: tbss_2_reg [options]

Target-selection options - choose ONE of:
 -T            : use FMRIB58_FA_1mm as target for nonlinear registrations (recommended)
 -t <target>   : use <target> image as target for nonlinear registrations
 -n            : find best target from all images in FA

EOF
    exit 1
}

do_reg(){

    f=$1

    for g in `$FSLDIR/bin/imglob *_FA.*` ; do
        	
	o=${g}_to_$f
	
	if [ ! -f ${o}_warp.msf ] ; then
	    echo $o
	    touch ${o}_warp.msf
	    echo "$FSLDIR/bin/fsl_reg $g $f ${g}_to_$f -e -FA" >> .commands
	fi
	
    done
}

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

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

/bin/rm -f FA/.commands

if [ $1 = -n ] ; then
    cd FA
    for f in `$FSLDIR/bin/imglob *_FA.*` ; do
	do_reg $f
    done
else
    if [ $1 = -T ] ; then
	TARGET=$FSLDIR/data/standard/FMRIB58_FA_1mm
    elif [ $1 = -t ] ; then
	TARGET=$2
    else
	Usage
    fi
    if [ `${FSLDIR}/bin/imtest $TARGET` = 0 ] ; then
	echo ""
	echo "Error: target image $TARGET not valid"
	Usage
    fi
    $FSLDIR/bin/imcp $TARGET FA/target
    cd FA
    do_reg target
fi

${FSLDIR}/bin/fsl_sub -l tbss_logs -T 60 -N tbss_2_reg -t .commands