MRILIB Namespace Reference

MRI volume and coordinate-system I/O (volumes, voxel geometry, transforms). More...

Classes
class	MriCorFifIO
	COR.fif FIFF file writer. More...
class	MriCorIO
	FreeSurfer COR slice file reader. More...
class	MriMghIO
	FreeSurfer MGH/MGZ file reader. More...
struct	MriSlice
	Single MRI slice data. More...
class	MriVolData
	MRI volume data from FreeSurfer MGH/MGZ file. More...

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

MRI volume and coordinate-system I/O (volumes, voxel geometry, transforms).

Function Documentation

buildDateTime()

const char * MRILIB::buildDateTime

(

)

Returns the build date and time.

Definition at line 45 of file mri_global.cpp.

buildHash()

const char * MRILIB::buildHash

(

)

Returns the short git hash.

Definition at line 46 of file mri_global.cpp.

buildHashLong()

const char * MRILIB::buildHashLong

(

)

Returns the long git hash.

Definition at line 47 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 142 of file mri_types.h.

COR_NSLICE

int MRILIB::COR_NSLICE = 256

constexpr

Number of COR slices.

Definition at line 140 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 143 of file mri_types.h.

COR_WIDTH

int MRILIB::COR_WIDTH = 256

constexpr

Width of each COR slice in pixels.

Definition at line 141 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 126 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 125 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 124 of file mri_types.h.

MRI_ALL_FRAMES

int MRILIB::MRI_ALL_FRAMES = -1

constexpr

Load all frames.

Definition at line 91 of file mri_types.h.

MRI_BITMAP

int MRILIB::MRI_BITMAP = 5

constexpr

Bitmap (unused in practice).

Definition at line 80 of file mri_types.h.

MRI_FLOAT

int MRILIB::MRI_FLOAT = 3

constexpr

32-bit float.

Definition at line 78 of file mri_types.h.

MRI_INT

int MRILIB::MRI_INT = 1

constexpr

Signed 32-bit integer.

Definition at line 76 of file mri_types.h.

MRI_LONG

int MRILIB::MRI_LONG = 2

constexpr

Long integer (unused in practice).

Definition at line 77 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 107 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 110 of file mri_types.h.

MRI_MGH_VERSION

int MRILIB::MRI_MGH_VERSION = 1

constexpr

Current MGH file format version.

Definition at line 57 of file mri_types.h.

MRI_NO_FRAMES

int MRILIB::MRI_NO_FRAMES = -2

constexpr

Do not load data at all.

Definition at line 92 of file mri_types.h.

MRI_SHORT

int MRILIB::MRI_SHORT = 4

constexpr

Signed 16-bit short.

Definition at line 79 of file mri_types.h.

MRI_TENSOR

int MRILIB::MRI_TENSOR = 6

constexpr

Tensor (unused in practice).

Definition at line 81 of file mri_types.h.

MRI_UCHAR

int MRILIB::MRI_UCHAR = 0

constexpr

Unsigned char (8-bit).

Definition at line 75 of file mri_types.h.