#!/bin/sh

# BAYCEST: Bayesican analysis for chemical exchange saturation transfer
#
# Michael Chappell, QuBIC & FMRIB Image Analysis Groups
#
# Copyright (c) 2011-2012 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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#   
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#   commercially. Use for which any financial return is received shall be
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#   innovation@isis.ox.ac.uk quoting reference DE/9564.
export LC_NUMERIC=C

Usage() {
echo "Bayesian analysis for chemical exchange saturation transfer z-spectra"
echo ""
echo "Usage:"
echo " --data=        : specify data file (nifti image)"
echo " --mask=        : specify mask file (nifiti image)"
echo " --output=      : specify output directory name"
echo " --pools=       : specify pools to be included in model (ascii matrix)"
echo " --spec=        : data specification (ascii matrix)"
echo " --ptrain=      : specify pulse shape (ascii matrix)"
echo ""
echo "Options:"
echo " --spatial      : Use spatial prior (appropriate for in vivo data)"
echo " --t12prior     : include uncertainty in T1 and T2 values"
echo ""
}

# deal with options
if [ -z $1 ]; then
    Usage
    exit 1
fi

fabbercmd=""
until [ -z $1 ]; do
    case $1 in
	--spatial)   spatial=1
	    ;;
	--t12prior)  fabbercmd=$fabbercmd" --t12prior"
	    ;;
	*)   
	    fabbercmd=$fabbercmd" $1" 
            # in this case just add the command to those to pass to fabber
	    ;;
    esac
    shift
done

#where to find fabber
fabber=fabber

# what VB mode?
if [ -z $spatial ]; then
    fabbercmd=$fabbercmd" --method=vb"
else
    fabbercmd=$fabbercmd" --method=spatialvb --param-spatial-priors=MN+"
fi
echo "$fabbercmd"

$fabber --noise=white --model=cest --data-order=singlefile --max-iterations=20 --save-model-fit $fabbercmd