/*  BET - Brain Extraction Tool

    BETv1 Steve Smith
    BETv2 Mickael Pechaud, Mark Jenkinson, Steve Smith
    FMRIB Image Analysis Group

    Copyright (C) 1999-2003 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
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    You are not permitted under this Licence to use this Software
    commercially. Use for which any financial return is received shall be
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    by or on behalf of Licensee to third parties or (2) use of the
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    (3) use of the Software or any derivative of it for research with the
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#ifndef _t1only
#define _t1only

#include "meshclass/meshclass.h"
#include "newimage/newimageall.h"
#include "utils/options.h"

using namespace mesh;
using namespace NEWIMAGE;
using namespace Utilities;
using namespace std;

struct trMatrix
{
  double m11, m12, m13, m14, m21, m22, m23, m24, m31, m32, m33, m34, m41, m42, m43, m44;
};

volume<short> default_volume;

void draw_segment(volume<short>& image, const Pt& p1, const Pt& p2);

void draw_mesh(volume<short>& image, const Mesh &m);

volume<short> make_mask_from_mesh(const volume<short> & image, const Mesh& m);

double standard_step_of_computation(const volume<float> & image, Mesh & m, const int iteration_number, const double E,const double F, const float addsmooth, const float speed, const int nb_iter, const int id=5, const int od=15, const bool vol=false, const volume<short> & mask=default_volume);

vector<double> t1only_special_extract(const volume<float> & t1, const Pt & point, const Vec & n) ;

vector<double> t1only_co_ext(const volume<float> & t1, const Pt & point, const Vec & n) ;

void t1only_write_ext_skull(volume<float> & output_inskull, volume<float> & output_outskull, volume<float> & output_outskin, const volume<float> & t1, const Mesh & m, const trMatrix & M) ;

int t1only_main(int argc, char *argv[], int nb_pars, OptionParser & options);

vector<double> special_extract(const volume<float> & t1, const volume<float> & t2, const Pt & point, const Vec & n, volume<short> & csfvolume);

vector<double> co_ext(const volume<float> & t1, const volume<float> & t2, const Pt & point, const Vec & n, volume<short> & csfvolume);

bool special_case(const Pt & point, const Vec & n, const trMatrix & M);

void write_ext_skull(volume<float> & output_inskull, volume<float> & output_outskull, volume<float> & output_outskin, const volume<float> & t1, const volume<float> & t2, const Mesh & m, const trMatrix & M, volume<short> & csfvolume);


#endif