/* filmbabe_vb_flobs.h Mark Woolrich, FMRIB Image Analysis Group Copyright (C) 1999-2000 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"). 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Contact details are: innovation@isis.ox.ac.uk quoting reference DE/9564. */ #if !defined(filmbabe_vb_flobs_h) #define filmbabe_vb_flobs_h #include #include #include "newmatap.h" #include "newmatio.h" #include "newimage/newimageall.h" #include "utils/tracer_plus.h" #include "filmbabeoptions.h" #include "connected_offset.h" #include "miscmaths/sparse_matrix.h" using namespace NEWMAT; using namespace NEWIMAGE; namespace Filmbabe { class Voxel { public: int x; int y; int z; Voxel(int px, int py, int pz) : x(px),y(py),z(pz){} bool operator==(const Voxel& r) const {return (x==r.x && y==r.y && z==r.z);} bool is_neighbour(const Voxel& r) const {return ((x==r.x-1 && y==r.y && z==r.z)|| (x==r.x+1 && y==r.y && z==r.z)|| (x==r.x && y==r.y-1 && z==r.z)|| (x==r.x && y==r.y+1 && z==r.z)|| (x==r.x && y==r.y && z==r.z-1)|| (x==r.x && y==r.y && z==r.z+1)) ;} }; class Filmbabe_Vb_Flobs { public: // Constructor Filmbabe_Vb_Flobs(const volume4D& pdata, const volume& pmask, const Matrix& pdesignmatrix, const ColumnVector& pflobsregressors, const volume4D& plocalweights, const vector& pconnected_offsets, int pnum_superthreshold); // setup void setup(); // run void run(); // save data to logger dir void save() ; // Destructor virtual ~Filmbabe_Vb_Flobs(){} private: Filmbabe_Vb_Flobs(); const Filmbabe_Vb_Flobs& operator=(Filmbabe_Vb_Flobs&); Filmbabe_Vb_Flobs(Filmbabe_Vb_Flobs&); void process_flobsregressors(); void update_Beta(); void update_A(); void update_phiA(); void update_phie(); void update_phiBeta(); int xsize; int ysize; int zsize; int ntpts; // num flobs Original evs int nflobsevs; // num basis functions for each flobs Original evs (is the same for all Original evs) int nbfs; // num of non flobs evs int nnonflobsevs; // total number of actual real evs in design matrix int nrealevs; const volume4D& data; const volume& mask; Matrix designmatrix; const ColumnVector& flobsregressors; Matrix QtXXt; const volume4D& localweights; const vector& connected_offsets; volume indices; vector voxels; Matrix Y; // Prior distribution params // m_Beta_0(e) ColumnVector m_Beta_0_global; SymmetricMatrix lambda_Beta_0_global; vector m_Beta_0; vector lambda_Beta_0; SparseMatrix D; ColumnVector trace_ilambdaDA; vector trace_ilambdaBeta; ColumnVector trace_ilambdaXXt; vector diag_ilambdaA; // Posterior distribution params // q(Beta)~MVN(m_Beta,lambda_Beta); // m_Beta[i]((bf-1)*nevs+e) vector m_Beta; vector ilambda_Beta; // q(A_p)~MVN(m_A_p,lambda_A_p); // m_A[p](i) vector m_A; // q(phi_Beta)~Ga(b_Beta,c_Beta); // gam_Beta = gam(c_Beta+1)/gam(c_Beta) // gam_Beta[i](e) vector gam_Beta; // q(phi_A_p)~Ga(b_A_p,c_A_p); // gam_A_p = gam(c_A_p+1)/gam(c_A_p) ColumnVector gam_A; // q(phi_e)~Ga(b_e,c_e); // gam_e = gam(c_e+1)/gam(c_e) ColumnVector gam_e; int num_superthreshold; int maxnumneighs; int ntar; int count; vector ilambdaDA; vector ilambdaA; int niters; Matrix realevcoord; vector QemReCquad; vector Re; vector Qe; Matrix Q; Matrix designmatrixQ; vector gamAhist; }; } #endif