Functions
template<class MatrixType >
void	check (const MatrixType &PE)
	check that a phase-encoding table is valid More...

template<class MatrixType , class HeaderType >
void	check (const MatrixType &PE, const HeaderType &header)
	check that the PE scheme matches the DWI data in header More...

template<class MatrixType >
void	set_scheme (Header &header, const MatrixType &PE)
	store the phase encoding matrix in a header More...

void	clear_scheme (Header &header)
	clear the phase encoding matrix from a header More...

Eigen::MatrixXd	parse_scheme (const Header &)
	parse the phase encoding matrix from a header More...

Eigen::MatrixXd	get_scheme (const Header &)
	get a phase encoding matrix More...

template<class MatrixType >
void	scheme2eddy (const MatrixType &PE, Eigen::MatrixXd &config, Eigen::Array< int, Eigen::Dynamic, 1 > &indices)
	Convert a phase-encoding scheme into the EDDY config / indices format. More...

Eigen::MatrixXd	eddy2scheme (const Eigen::MatrixXd &, const Eigen::Array< int, Eigen::Dynamic, 1 > &)
	Convert phase-encoding infor from the EDDY config / indices format into a standard scheme. More...

template<class MatrixType , class HeaderType >
Eigen::MatrixXd	transform_for_image_load (const MatrixType &pe_scheme, const HeaderType &H)
	Modifies a phase encoding scheme if being imported alongside a non-RAS image. More...

template<class MatrixType , class HeaderType >
Eigen::MatrixXd	transform_for_nifti_write (const MatrixType &pe_scheme, const HeaderType &H)
	Modifies a phase encoding scheme if being exported alongside a NIfTI image. More...

template<class MatrixType , class HeaderType >
void	save (const MatrixType &PE, const HeaderType &header, const std::string &path)
	Save a phase-encoding scheme to file. More...

template<class MatrixType , class HeaderType >
void	save_eddy (const MatrixType &PE, const HeaderType &header, const std::string &config_path, const std::string &index_path)
	Save a phase-encoding scheme to EDDY format config / index files. More...

void	export_commandline (const Header &)
	Save the phase-encoding scheme from a header to file depending on command-line options. More...

template<class HeaderType >
Eigen::MatrixXd	load (const std::string &path, const HeaderType &header)
	Load a phase-encoding scheme from a matrix text file. More...

template<class HeaderType >
Eigen::MatrixXd	load_eddy (const std::string &config_path, const std::string &index_path, const HeaderType &header)
	Load a phase-encoding scheme from an EDDY-format config / indices file pair. More...

Variables
const App::OptionGroup	ImportOptions

const App::OptionGroup	SelectOptions

const App::OptionGroup	ExportOptions

Function Documentation

◆ check() [1/2]

template<class MatrixType >

void MR::PhaseEncoding::check ( const MatrixType & PE )

check that a phase-encoding table is valid

Definition at line 46 of file phase_encoding.h.

◆ check() [2/2]

template<class MatrixType , class HeaderType >

void MR::PhaseEncoding::check	(	const MatrixType &	PE,
		const HeaderType &	header
	)

check that the PE scheme matches the DWI data in header

Definition at line 66 of file phase_encoding.h.

◆ clear_scheme()

void MR::PhaseEncoding::clear_scheme ( Header & header )

clear the phase encoding matrix from a header

this will delete any trace of phase encoding information from the Header::keyval() structure of header.

◆ eddy2scheme()

Eigen::MatrixXd MR::PhaseEncoding::eddy2scheme	(	const Eigen::MatrixXd &	,
		const Eigen::Array< int, Eigen::Dynamic, 1 > &
	)

Convert phase-encoding infor from the EDDY config / indices format into a standard scheme.

◆ export_commandline()

void MR::PhaseEncoding::export_commandline ( const Header & )

Save the phase-encoding scheme from a header to file depending on command-line options.

◆ get_scheme()

Eigen::MatrixXd MR::PhaseEncoding::get_scheme ( const Header & )

get a phase encoding matrix

get a valid phase-encoding matrix, either from files specified at the command-line, or from the contents of the image header.

◆ load()

template<class HeaderType >

Eigen::MatrixXd MR::PhaseEncoding::load	(	const std::string &	path,
		const HeaderType &	header
	)

Load a phase-encoding scheme from a matrix text file.

Definition at line 308 of file phase_encoding.h.

◆ load_eddy()

template<class HeaderType >

Eigen::MatrixXd MR::PhaseEncoding::load_eddy	(	const std::string &	config_path,
		const std::string &	index_path,
		const HeaderType &	header
	)

Load a phase-encoding scheme from an EDDY-format config / indices file pair.

Definition at line 321 of file phase_encoding.h.

◆ parse_scheme()

Eigen::MatrixXd MR::PhaseEncoding::parse_scheme ( const Header & )

parse the phase encoding matrix from a header

extract the phase encoding matrix stored in the header if one is present. This is expected to be stored in the Header::keyval() structure, under the key 'pe_scheme'. Alternatively, if the phase encoding direction and bandwidth is fixed for all volumes in the series, this information may be stored using the keys 'PhaseEncodingDirection' and 'TotalReadoutTime'.

◆ save()

template<class MatrixType , class HeaderType >

void MR::PhaseEncoding::save	(	const MatrixType &	PE,
		const HeaderType &	header,
		const std::string &	path
	)

Save a phase-encoding scheme to file.

Definition at line 273 of file phase_encoding.h.

◆ save_eddy()

template<class MatrixType , class HeaderType >

void MR::PhaseEncoding::save_eddy	(	const MatrixType &	PE,
		const HeaderType &	header,
		const std::string &	config_path,
		const std::string &	index_path
	)

Save a phase-encoding scheme to EDDY format config / index files.

Definition at line 290 of file phase_encoding.h.

◆ scheme2eddy()

template<class MatrixType >

void MR::PhaseEncoding::scheme2eddy	(	const MatrixType &	PE,
		Eigen::MatrixXd &	config,
		Eigen::Array< int, Eigen::Dynamic, 1 > &	indices
	)

Convert a phase-encoding scheme into the EDDY config / indices format.

Definition at line 160 of file phase_encoding.h.

◆ set_scheme()

template<class MatrixType >

void MR::PhaseEncoding::set_scheme	(	Header &	header,
		const MatrixType &	PE
	)

store the phase encoding matrix in a header

this will store the phase encoding matrix into the Header::keyval() structure of header.

If the phase encoding direction and/or total readout time varies between volumes, then the information will be stored in field "pe_scheme"; if not, it will instead be stored in fields "PhaseEncodingDirection" and "TotalReadoutTime"

Definition at line 90 of file phase_encoding.h.

◆ transform_for_image_load()

template<class MatrixType , class HeaderType >

Eigen::MatrixXd MR::PhaseEncoding::transform_for_image_load	(	const MatrixType &	pe_scheme,
		const HeaderType &	H
	)

Modifies a phase encoding scheme if being imported alongside a non-RAS image.

Definition at line 199 of file phase_encoding.h.

◆ transform_for_nifti_write()

template<class MatrixType , class HeaderType >

Eigen::MatrixXd MR::PhaseEncoding::transform_for_nifti_write	(	const MatrixType &	pe_scheme,
		const HeaderType &	H
	)

Modifies a phase encoding scheme if being exported alongside a NIfTI image.

Definition at line 227 of file phase_encoding.h.

Variable Documentation

◆ ExportOptions

const App::OptionGroup MR::PhaseEncoding::ExportOptions

extern

◆ ImportOptions

const App::OptionGroup MR::PhaseEncoding::ImportOptions

extern

◆ SelectOptions

const App::OptionGroup MR::PhaseEncoding::SelectOptions

extern

Functions

Variables

Function Documentation

◆ check() [1/2]

◆ check() [2/2]

◆ clear_scheme()

◆ eddy2scheme()

◆ export_commandline()

◆ get_scheme()

◆ load()

◆ load_eddy()

◆ parse_scheme()

◆ save()

◆ save_eddy()

◆ scheme2eddy()

◆ set_scheme()

◆ transform_for_image_load()

◆ transform_for_nifti_write()

Variable Documentation

◆ ExportOptions

◆ ImportOptions

◆ SelectOptions