#!/bin/sh 

#   concat_bvars - script to concatenate .bvars file that are output from 
#   "first". The script retains a single header and keeps track of the number 
#   subjects. All bvars should correspond to the same model.  
#
#   Brian Patenaude and Mark Jenkinson, FMRIB Image Analysis Group
#
#   Copyright (C) 2006-2009 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")
#   
#   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.
#   
#   The Licensee agrees to indemnify the University and hold the
#   University harmless from and against any and all claims, damages and
#   liabilities asserted by third parties (including claims for
#   negligence) which arise directly or indirectly from the use of the
#   Software or the sale of any products based on the Software.
#   
#   No part of the Software may be reproduced, modified, transmitted or
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#   without the express permission of the University. The permission of
#   the University is not required if the said reproduction, modification,
#   transmission or transference is done without financial return, the
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#   product, and all original and amended source code is included in any
#   transmitted product. You may be held legally responsible for any
#   copyright infringement that is caused or encouraged by your failure to
#   abide by these terms and conditions.
#   
#   You are not permitted under this Licence to use this Software
#   commercially. Use for which any financial return is received shall be
#   defined as commercial use, and includes (1) integration of all or part
#   of the source code or the Software into a product for sale or license
#   by or on behalf of Licensee to third parties or (2) use of the
#   Software or any derivative of it for research with the final aim of
#   developing software products for sale or license to a third party or
#   (3) use of the Software or any derivative of it for research with the
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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

Usage() {
    echo ""
    echo "Usage:   concat_bvars <output_bvars.bvars> <list_of_input_bvars>"
    echo ""
    echo "e.g.:  concat_bvars lhipp_all.bvars sub1_lhipp.bvars sub2_lhipp.bvars ... subN_lhipp.bvars"
    echo ""
}

Usage_and_exit() {
    Usage
    exit
}

[ "${1}_" = "_"  ] && Usage_and_exit

output=$1;
shift;
#echo "make sure all bvar files use the same model!!!!"

if [ -f $output ] ; then
    Usage
    echo " "
    echo "ERROR: Output file already exists!"
    echo "Check the above usage and, if necssary, remove this file before running"
    exit 1
fi

listfile=`$FSLDIR/bin/tmpnam`_bvars
if [ -f ${listfile}.txt ] ; then rm -f ${listfile}.txt ; fi
touch ${listfile}.txt
for fn in $@ ; do
  echo $fn >> ${listfile}.txt
done
$FSLDIR/bin/first_utils --concatBvars -i ${listfile}.txt -o $output
rm -f ${listfile}.txt
