MRILIB Namespace Reference

Volume I/O, voxel geometry and slice resampling for structural MRI data inside mne-cpp. More...

Classes
class	MriCorFifIO
	Stateless serialiser that turns an MriVolData into a FIFF MRI set (COR.fif). More...
class	MriCorIO
	Stateless reader for the FreeSurfer COR-NNN directory layout. More...
class	MriMghIO
	Stateless decoder for FreeSurfer MGH and MGZ volume containers. More...
class	MriNiftiIO
	Stateless decoder for NIfTI-1 single-file volumes (.nii and .nii.gz). More...
struct	MriSliceImage
	Single 2D MRI cross-section produced by MriSlicer (pixel buffer + RAS metadata). More...
class	MriSlicer
	Orthogonal-plane resampler (axial / coronal / sagittal) from MriVolData to MriSliceImage. More...
struct	MriSlice
	Single 2D MRI slice (pixels + slice→RAS transform) used as the volume's storage unit. More...
class	MriVolData
	Format-agnostic 3D MRI volume: header geometry, voxel buffer (as a vector of MriSlice), scan parameters and provenance. More...

Enumerations
enum class	SliceOrientation { Axial , Coronal , Sagittal }

Functions
const char *	buildDateTime ()
const char *	buildHash ()
const char *	buildHashLong ()

Variables
MGH Format Version
constexpr int	MRI_MGH_VERSION = 1
MGH Voxel Data Types
Data type codes for voxels in MGH/MGZ files. From FreeSurfer mri.h and MNE C mne_types_mne-c.h. See: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat "type: data type of the image buffer; can be one of the following: UCHAR, SHORT, INT, or FLOAT (specified as 0, 4, 1, or 3, respectively)"
constexpr int	MRI_UCHAR = 0
constexpr int	MRI_INT = 1
constexpr int	MRI_LONG = 2
constexpr int	MRI_FLOAT = 3
constexpr int	MRI_SHORT = 4
constexpr int	MRI_BITMAP = 5
constexpr int	MRI_TENSOR = 6
Frame Loading Constants
constexpr int	MRI_ALL_FRAMES = -1
constexpr int	MRI_NO_FRAMES = -2
MGH Header Constants
Fixed offsets and sizes in the MGH file header. See: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
constexpr int	MRI_MGH_DATA_OFFSET = 284
constexpr int	MRI_MGH_HEADER_FIXED_SIZE = 30
MGH Footer Tag Types
Tag identifiers found in the MGH footer after the voxel data. From FreeSurfer tags.h.
constexpr int	MGH_TAG_OLD_SURF_GEOM = 20
constexpr int	MGH_TAG_OLD_MGH_XFORM = 30
constexpr int	MGH_TAG_MGH_XFORM = 31
COR Slice Constants
Fixed dimensions for FreeSurfer COR slice files. COR files contain 256 coronal slices of 256×256 unsigned chars at 1mm isotropic.
constexpr int	COR_NSLICE = 256
constexpr int	COR_WIDTH = 256
constexpr int	COR_HEIGHT = 256
constexpr float	COR_PIXEL_SIZE = 1e-3f

Detailed Description

Volume I/O, voxel geometry and slice resampling for structural MRI data inside mne-cpp.

Hosts every public type that participates in loading a 3D MRI volume (MGH/MGZ, NIfTI-1, FreeSurfer COR), describing it in memory (MriVolData, MriSlice), resampling it onto an orthogonal viewing plane (MriSlicer, MriSliceImage) and re-serialising it through the FIFF MRI block hierarchy (MriCorFifIO).

Enumeration Type Documentation

SliceOrientation

enum class MRILIB::SliceOrientation

strong

Slice orientation for orthogonal MRI volume slicing.

Enumerator
Axial
Coronal
Sagittal

Definition at line 75 of file mri_slicer.h.

Function Documentation

buildDateTime()

const char * MRILIB::buildDateTime

(

)

Returns the build date and time.

Definition at line 30 of file mri_global.cpp.

buildHash()

const char * MRILIB::buildHash

(

)

Returns the short git hash.

Definition at line 31 of file mri_global.cpp.

buildHashLong()

const char * MRILIB::buildHashLong

(

)

Returns the long git hash.

Definition at line 32 of file mri_global.cpp.

Variable Documentation

COR_HEIGHT

int MRILIB::COR_HEIGHT = 256

constexpr

Height of each COR slice in pixels.

Definition at line 135 of file mri_types.h.

COR_NSLICE

int MRILIB::COR_NSLICE = 256

constexpr

Number of COR slices.

Definition at line 133 of file mri_types.h.

COR_PIXEL_SIZE

float MRILIB::COR_PIXEL_SIZE = 1e-3f

constexpr

Pixel size for COR slices (1mm in meters).

Definition at line 136 of file mri_types.h.

COR_WIDTH

int MRILIB::COR_WIDTH = 256

constexpr

Width of each COR slice in pixels.

Definition at line 134 of file mri_types.h.

MGH_TAG_MGH_XFORM

int MRILIB::MGH_TAG_MGH_XFORM = 31

constexpr

MGH Talairach transform tag (contains path to .xfm file).

Definition at line 119 of file mri_types.h.

MGH_TAG_OLD_MGH_XFORM

int MRILIB::MGH_TAG_OLD_MGH_XFORM = 30

constexpr

Old MGH transform tag.

Definition at line 118 of file mri_types.h.

MGH_TAG_OLD_SURF_GEOM

int MRILIB::MGH_TAG_OLD_SURF_GEOM = 20

constexpr

Old surface geometry tag.

Definition at line 117 of file mri_types.h.

MRI_ALL_FRAMES

int MRILIB::MRI_ALL_FRAMES = -1

constexpr

Load all frames.

Definition at line 84 of file mri_types.h.

MRI_BITMAP

int MRILIB::MRI_BITMAP = 5

constexpr

Bitmap (unused in practice).

Definition at line 73 of file mri_types.h.

MRI_FLOAT

int MRILIB::MRI_FLOAT = 3

constexpr

32-bit float.

Definition at line 71 of file mri_types.h.

MRI_INT

int MRILIB::MRI_INT = 1

constexpr

Signed 32-bit integer.

Definition at line 69 of file mri_types.h.

MRI_LONG

int MRILIB::MRI_LONG = 2

constexpr

Long integer (unused in practice).

Definition at line 70 of file mri_types.h.

MRI_MGH_DATA_OFFSET

int MRILIB::MRI_MGH_DATA_OFFSET = 284

constexpr

Fixed byte offset where image data begins (bytes 0-283 are header).

Definition at line 100 of file mri_types.h.

MRI_MGH_HEADER_FIXED_SIZE

int MRILIB::MRI_MGH_HEADER_FIXED_SIZE = 30

constexpr

Size of the fixed portion of the header (before RAS info).

Definition at line 103 of file mri_types.h.

MRI_MGH_VERSION

int MRILIB::MRI_MGH_VERSION = 1

constexpr

Current MGH file format version.

Definition at line 50 of file mri_types.h.

MRI_NO_FRAMES

int MRILIB::MRI_NO_FRAMES = -2

constexpr

Do not load data at all.

Definition at line 85 of file mri_types.h.

MRI_SHORT

int MRILIB::MRI_SHORT = 4

constexpr

Signed 16-bit short.

Definition at line 72 of file mri_types.h.

MRI_TENSOR

int MRILIB::MRI_TENSOR = 6

constexpr

Tensor (unused in practice).

Definition at line 74 of file mri_types.h.

MRI_UCHAR

int MRILIB::MRI_UCHAR = 0

constexpr

Unsigned char (8-bit).

Definition at line 68 of file mri_types.h.