tbss_2_reg

#!/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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#   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.
export LC_ALL=C

FSL_SUB=/usr/share/fsl/overlay/fsl_sub

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=$1
    shift
    all_list=$*

    for g in $all_list; do
        o=${g}_to_$f
        echo "$FSLDIR/bin/fsl_reg $g $f ${g}_to_$f -e -FA " >> .commands
    done
}

[ x"$1" = "x" ] || [ "$1" = "-h" ] && Usage

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

/bin/rm -f FA/.commands*

if [ $1 = -n ] ; then
    cd FA
    chunksize=8
    all_list=$($FSLDIR/bin/imglob *_FA.*)
    # prepare commands _before_ submission so temporary output won't
    # affect $(imglob *_FA.*)
    for f in $all_list; do
	    do_reg $f $all_list
    done
else
    chunksize=1
    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 $TARGET FA/target
    cd FA
    all_list=$($FSLDIR/bin/imglob *_FA.*)
    do_reg target $all_list
fi

$FSL_SUB -l tbss_logs -T 60 -N tbss_2_reg -t .commands -c $chunksize -B