#!/bin/sh

#   Copyright (C) 2004 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 4.0 (c) 2007, 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
#   transferred in any form or by any means, electronic or mechanical,
#   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
#   conditions of this Licence are imposed upon the receiver of the
#   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
#   final aim of developing non-software products for sale or license to a
#   third party, or (4) use of the Software to provide any service to an
#   external organisation for which payment is received. If you are
#   interested in using the Software commercially, please contact Isis
#   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/1112.

Usage() {
    echo ""
    echo "Usage: bedpostX_proc <subject_dir> <nslices> [-n nfibres -w ard_weight -b burnin_period] [piddir]"
    echo ""
    exit
}


[ "$2" = "" ] && Usage


subjdir=$1
nslices=$2


#parse option arguments
nfibres=2
fudge=1.5
burnin=2000
while [ ! -z "$3" ]
do
  case "$3" in
      -n) nfibres=$4;shift;;
      -w) fudge=$4;shift;;
      -b) burnin=$4;shift;;
      *) piddir=$3;;
  esac
  shift
done

echo subjdir $subjdir
echo nslices $nslices
echo nfibres $nfibres
echo fudge $fudge
echo burnin $burnin
echo piddir $piddir

[ "$piddir" = "" ] || touch ${piddir}/`hostname`_fdt_${$}


slice=0
while [ $slice -lt $nslices ];do
    slicezp=`${FSLDIR}/bin/zeropad $slice 4`
    if [ ! -f ${subjdir}.bedpostX/logs/.$slicezp ] ; then
	echo `hostname`_${$} > ${subjdir}.bedpostX/logs/.$slicezp
	sleep 10
	if [ `hostname`_${$} = `cat ${subjdir}.bedpostX/logs/.$slicezp | sed -n '1p'` ] ; then
	    nice ${FSLDIR}/bin/xfibres --data=$subjdir/data_slice_$slicezp --mask=$subjdir/nodif_brain_mask_slice_$slicezp -b $subjdir/bvals -r $subjdir/bvecs --forcedir --logdir=$subjdir.bedpostX/diff_slices/data_slice_$slicezp --nj=1000 --bi=$burnin --bn=0 --se=20 --nfibres=$nfibres --fudge=$fudge > $subjdir.bedpostX/logs/log$slicezp 

	    touch ${subjdir}.bedpostX/logs/.${slicezp}_finished
	fi
    fi
    slice=`echo "$slice + 1" | bc`
done

[ "$piddir" = "" ] || rm ${piddir}/`hostname`_fdt_${$}
sleep 10
