// Utility for resampling of DTI data using fields/data // estimated by topup. // // applytopup.h // // Jesper Andersson, FMRIB Image Analysis Group // //Copyright (C) 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"). 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Contact details are: innovation@isis.ox.ac.uk quoting reference DE/9564. */ #ifndef applytopup_h #define applytopup_h #include #include "newmat.h" #include "miscmaths/miscmaths.h" #include "newimage/newimageall.h" #include "warpfns/fnirt_file_reader.h" #include "topup_file_io.h" namespace TOPUP { class ApplyTopupException: public std::exception { private: std::string m_msg; public: ApplyTopupException(const std::string& msg) throw(): m_msg(msg) {} virtual const char * what() const throw() { return string("ApplyTopup:: msg=" + m_msg).c_str(); } ~ApplyTopupException() throw() {} }; // Helper-class for divding a set of scans into collections that can be used for least squares restoration class TopupCollections { public: TopupCollections(const std::vector& indx, const TopupDatafileReader& dfile); ~TopupCollections() {} unsigned int NCollections() { return(indxs.size()); } unsigned int NIndices(unsigned int c) { if (c>=NCollections()) throw ApplyTopupException("TopupCollections::NIndicies: Index out of range"); else return(indxs[c].size()); } unsigned int NScans(unsigned int c) { return(NIndices(c)); } unsigned int IndexAt(unsigned int c, unsigned int i); unsigned int ScanAt(unsigned int c, unsigned int i); private: std::vector > indxs; std::vector > scans; }; // Global functions used by applytopup // Does the job int applytopup(); // Helper functions NEWIMAGE::volume4D vb_resample_4D(const TopupDatafileReader& datafile, const TopupFileReader& topupfile, const std::vector& inindices, NEWIMAGE::volume& mask, std::vector >& scans); NEWIMAGE::volume4D vb_resample_3D(const TopupDatafileReader& datafile, const TopupFileReader& topupfile, const std::vector& inindices, NEWIMAGE::volume& mask, std::vector >& scans); double tau_update_contrib(const std::vector >& mu, const std::vector > >& Lambda, const std::vector > >& Lijk); double tau_update(const std::vector > >& mu, const std::vector > >& Lambda, const std::vector > >& Lijk, double tau_0); double tau_update(const std::vector >& mu, const std::vector > >& Lambda, const std::vector > >& Lijk, double tau_0); NEWMAT::ColumnVector mu_update(const std::vector >& mu, const MISCMATHS::SpMat& K, const NEWMAT::ColumnVector& y, const NEWMAT::CroutMatrix& Lambda, const std::vector > >& Lijk, double phi, double lambda, int sl, int row); NEWIMAGE::volume4D vb_resample_2D(const TopupDatafileReader& datafile, const TopupFileReader& topupfile, const std::vector& inindices, NEWIMAGE::volume& mask, std::vector >& scans); std::vector > > GetLijk(int sz, const std::vector sf); std::vector > GetLij(int sz, double sf); MISCMATHS::SpMat GetLii(int sz); NEWIMAGE::volume4D jac_resample(const TopupDatafileReader& datafile, const TopupFileReader& topupfile, const std::vector& inindices, NEWIMAGE::volume& mask, std::vector >& scans, NEWIMAGE::interpolation interp); NEWIMAGE::volume4D lsr_resample(const TopupDatafileReader& datafile, const TopupFileReader& topupfile, const std::vector& inindices, NEWIMAGE::volume& mask, std::vector >& scans); void resample_using_movement_parameters(const TopupDatafileReader& datafile, const TopupFileReader& topupfile, const std::vector& inindices, NEWIMAGE::volume& mask, std::vector >& scans, NEWIMAGE::interpolation interp); std::vector parse_commaseparated_numbers(const std::string& list); std::vector parse_commaseparated_list(const std::string& list); bool row_col_is_alright(const NEWIMAGE::volume& mask, unsigned int k, unsigned int ij, bool row); NEWMAT::ReturnMatrix extract_row_col(const NEWIMAGE::volume& vol, unsigned int k, unsigned int ij, bool row); void add_to_slice(NEWIMAGE::volume& vol, const std::vector& mu, unsigned int sl, bool row); void add_to_rows_cols(NEWIMAGE::volume4D& vol, const NEWMAT::Matrix& B, unsigned int k, unsigned int ij, bool row); void zero_out_rows_cols(NEWIMAGE::volume4D& vol, const NEWMAT::Matrix& map, bool row); } // End namespace TOPUP #endif // End ifndef applytopup_h