gradient.h File Reference

#include "app.h"
#include "header.h"
#include "dwi/shells.h"
#include "file/config.h"
#include "file/path.h"
#include "math/condition_number.h"
#include "math/sphere.h"
#include "math/SH.h"

Go to the source code of this file.

Namespaces
namespace	MR
namespace	MR::App
namespace	MR::DWI

Enumerations
enum class	MR::DWI::BValueScalingBehaviour { MR::DWI::Auto , MR::DWI::UserOn , MR::DWI::UserOff }

Functions
App::OptionGroup	MR::DWI::GradImportOptions ()
App::OptionGroup	MR::DWI::GradExportOptions ()
template<class MatrixType >
void	MR::DWI::check_DW_scheme (const Header &header, const MatrixType &grad)
	check that the DW scheme matches the DWI data in header More...
template<class MatrixType , class IndexVectorType >
Eigen::MatrixXd	MR::DWI::gen_direction_matrix (const MatrixType &grad, const IndexVectorType &dwi)
	convert the DW encoding matrix in grad into a azimuth/elevation direction set, using only the DWI volumes as per dwi More...
template<class MatrixType >
default_type	MR::DWI::condition_number_for_lmax (const MatrixType &dirs, int lmax)
Eigen::MatrixXd	MR::DWI::load_bvecs_bvals (const Header &header, const std::string &bvecs_path, const std::string &bvals_path)
	load and rectify FSL-style bvecs/bvals DW encoding files More...
void	MR::DWI::save_bvecs_bvals (const Header &, const std::string &, const std::string &)
	export gradient table in FSL format (bvecs/bvals) More...
template<class MatrixType >
void	MR::DWI::set_DW_scheme (Header &header, const MatrixType &G)
	store the DW gradient encoding matrix in a header More...
Eigen::MatrixXd	MR::DWI::parse_DW_scheme (const Header &header)
	parse the DW gradient encoding matrix from a header More...
Eigen::MatrixXd	MR::DWI::get_raw_DW_scheme (const Header &header)
	get the DW scheme as found in the headers or supplied at the command-line More...
void	MR::DWI::clear_DW_scheme (Header &)
	clear any DW gradient encoding scheme from the header More...
template<class MatrixType >
void	MR::DWI::stash_DW_scheme (Header &header, const MatrixType &grad)
	'stash' the DW gradient table More...
BValueScalingBehaviour	MR::DWI::get_cmdline_bvalue_scaling_behaviour ()
Eigen::MatrixXd	MR::DWI::get_DW_scheme (const Header &header, BValueScalingBehaviour bvalue_scaling=BValueScalingBehaviour::Auto)
	get the fully-interpreted DW gradient encoding matrix More...
void	MR::DWI::export_grad_commandline (const Header &header)
	process GradExportOptions command-line options More...
template<class MatrixType >
Eigen::MatrixXd	MR::DWI::compute_SH2amp_mapping (const MatrixType &directions, bool lmax_from_command_line=true, int default_lmax=8)
	get the matrix mapping SH coefficients to amplitudes More...
size_t	MR::DWI::lmax_for_directions (const Eigen::MatrixXd &directions, const bool lmax_from_command_line=true, const int default_lmax=8)
	get the maximum spherical harmonic order given a set of directions More...

Variables
App::Option	MR::DWI::bvalue_scaling_option
const char *const	MR::DWI::bvalue_scaling_description