MRILIB::MriVolData Class Reference

Format-agnostic 3D MRI volume: header geometry, voxel buffer (as a vector of MriSlice), scan parameters and provenance. More...

#include <mri_vol_data.h>

Public Member Functions
	MriVolData ()
bool	read (const QString &path)
bool	isValid () const
int	dimX () const
int	dimY () const
int	dimZ () const
QVector< int >	dims () const
QVector< float >	voxelDataAsFloat () const
Eigen::Matrix4f	computeVox2Ras () const
Eigen::Matrix4f	computeVox2RasTkr () const

Public Attributes
QString	fileName
int	version
int	width
int	height
int	depth
int	nframes
int	type
int	dof
bool	rasGood
float	xsize
float	ysize
float	zsize
Eigen::Vector3f	x_ras
Eigen::Vector3f	y_ras
Eigen::Vector3f	z_ras
Eigen::Vector3f	c_ras
FIFFLIB::FiffCoordTrans	voxelSurfRasT
float	TR
float	flipAngle
float	TE
float	TI
float	FoV
QString	talairachXfmPath
QVector< MriSlice >	slices

Detailed Description

Format-agnostic 3D MRI volume: header geometry, voxel buffer (as a vector of MriSlice), scan parameters and provenance.

The volume is the single in-memory representation every consumer in mne-cpp operates on, regardless of whether it was loaded from MGH/MGZ, NIfTI-1 or a FreeSurfer COR directory. Storage is decomposed into a vector of MriSlice so the COR.fif writer can serialise without an intermediate copy, while the slice viewer and the BEM coregistration step both index it through the same (column, row, slice) coordinate.

The header captures FreeSurfer's MGH conventions: voxel sizes (spacingX/Y/Z), direction cosines (Mdc, column-major), centre RAS (c_ras) and voxel data type (MRI_UCHAR / MRI_INT / MRI_FLOAT / MRI_SHORT). Optional scan parameters (TR, flip angle, TE, TI, FoV) and tags (Talairach transform path, provenance) round out the structure. The read() entry point dispatches on the file extension so callers do not need to branch on format.

Format reference: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat

Ported from mneMRIdataRec in MNE C (mne_types_mne-c.h) by Matti Hamalainen.

Definition at line 147 of file mri_vol_data.h.

Constructor & Destructor Documentation

MriVolData()

MriVolData::MriVolData

(

)

Default constructor.

Definition at line 52 of file mri_vol_data.cpp.

Member Function Documentation

computeVox2Ras()

Matrix4f MriVolData::computeVox2Ras

(

)

const

Builds the voxel-to-surface-RAS (MRI) 4×4 transform matrix.

Following FreeSurfer convention: M = Mdc * diag(xsize, ysize, zsize) P0 = c_ras - M * (dim/2) vox2ras = | M P0 | (in mm, converted to meters for FIFF) | 0 1 |

Returns

The 4×4 voxel-to-scanner-RAS transform in meters.

Definition at line 132 of file mri_vol_data.cpp.

computeVox2RasTkr()

Matrix4f MriVolData::computeVox2RasTkr

(

)

const

Builds the voxel-to-surface-RAS (tkRAS / tkregister) 4×4 transform.

Identical to computeVox2Ras() but forces c_ras = (0,0,0), producing the coordinate system used by FreeSurfer surfaces (lh.white, etc.).

Returns

The 4×4 voxel-to-tkRAS transform in meters.

Definition at line 179 of file mri_vol_data.cpp.

dims()

QVector< int > MRILIB::MriVolData::dims ( ) const

inline

Returns

Volume dimensions as {dimX, dimY, dimZ}.

Definition at line 209 of file mri_vol_data.h.

dimX()

int MRILIB::MriVolData::dimX ( ) const

inline

Returns

First (x) dimension — fastest-varying axis.

Definition at line 182 of file mri_vol_data.h.

dimY()

int MRILIB::MriVolData::dimY ( ) const

inline

Returns

Second (y) dimension.

Definition at line 191 of file mri_vol_data.h.

dimZ()

int MRILIB::MriVolData::dimZ ( ) const

inline

Returns

Third (z) dimension — slowest-varying axis.

Definition at line 200 of file mri_vol_data.h.

isValid()

bool MriVolData::isValid

(

)

const

Returns whether this volume contains valid data.

Returns

True if the volume has been loaded successfully.

Definition at line 78 of file mri_vol_data.cpp.

read()

bool MriVolData::read

(

const QString &

path

)

Convenience loader: reads an MGH/MGZ file and populates this volume.

Wraps MriMghIO::read() so callers don't need to manage a separate additionalTrans vector. Mirrors MNE-Python's nib.load(path) one-liner.

Parameters

[in]

path

Path to the .mgh or .mgz file.

Returns

True on success, false on error.

Definition at line 85 of file mri_vol_data.cpp.

voxelDataAsFloat()

QVector< float > MriVolData::voxelDataAsFloat

(

)

const

Returns all voxel data as a contiguous float array in x-fastest order.

Mirrors MNE-Python's img.get_fdata().ravel(order='F'). Regardless of the on-disk type (UCHAR, SHORT, INT, FLOAT) the output is always float. The array length is width * height * depth.

Returns

Flat voxel data; empty vector if the volume has no slices.

Definition at line 99 of file mri_vol_data.cpp.

Member Data Documentation

c_ras

Eigen::Vector3f MRILIB::MriVolData::c_ras

Center RAS coordinates (cr, ca, cs). Default: (0, 0, 0).

Definition at line 270 of file mri_vol_data.h.

depth

int MRILIB::MriVolData::depth

Third dimension (slowest).

Definition at line 259 of file mri_vol_data.h.

dof

int MRILIB::MriVolData::dof

Degrees of freedom.

Definition at line 262 of file mri_vol_data.h.

fileName

QString MRILIB::MriVolData::fileName

Name of the source file.

Definition at line 255 of file mri_vol_data.h.

flipAngle

float MRILIB::MriVolData::flipAngle

Flip angle (radians).

Definition at line 283 of file mri_vol_data.h.

FoV

float MRILIB::MriVolData::FoV

Field of view (unreliable per FreeSurfer docs).

Definition at line 286 of file mri_vol_data.h.

height

int MRILIB::MriVolData::height

Second dimension.

Definition at line 258 of file mri_vol_data.h.

nframes

int MRILIB::MriVolData::nframes

Number of frames (scalar components per voxel).

Definition at line 260 of file mri_vol_data.h.

rasGood

bool MRILIB::MriVolData::rasGood

Whether the direction cosines in the header are valid.

Definition at line 263 of file mri_vol_data.h.

slices

QVector<MriSlice> MRILIB::MriVolData::slices

Per-slice data (for COR-equivalent representation).

Definition at line 298 of file mri_vol_data.h.

talairachXfmPath

QString MRILIB::MriVolData::talairachXfmPath

Path to the Talairach .xfm file (from MGH footer tags).

Definition at line 292 of file mri_vol_data.h.

TE

float MRILIB::MriVolData::TE

Echo time (ms).

Definition at line 284 of file mri_vol_data.h.

TI

float MRILIB::MriVolData::TI

Inversion time (ms).

Definition at line 285 of file mri_vol_data.h.

TR

float MRILIB::MriVolData::TR

Repetition time (ms).

Definition at line 282 of file mri_vol_data.h.

type

int MRILIB::MriVolData::type

Voxel data type (MRI_UCHAR, MRI_INT, MRI_FLOAT, MRI_SHORT).

Definition at line 261 of file mri_vol_data.h.

version

int MRILIB::MriVolData::version

MGH format version (should be 1).

Definition at line 256 of file mri_vol_data.h.

voxelSurfRasT

FIFFLIB::FiffCoordTrans MRILIB::MriVolData::voxelSurfRasT

Voxel -> surface RAS (MRI) transform.

Definition at line 276 of file mri_vol_data.h.

width

int MRILIB::MriVolData::width

First dimension of the image buffer (fastest).

Definition at line 257 of file mri_vol_data.h.

x_ras

Eigen::Vector3f MRILIB::MriVolData::x_ras

X-direction cosines (xr, xa, xs). Default: (-1, 0, 0).

Definition at line 267 of file mri_vol_data.h.

xsize

float MRILIB::MriVolData::xsize

Voxel spacing in X direction (mm).

Definition at line 264 of file mri_vol_data.h.

y_ras

Eigen::Vector3f MRILIB::MriVolData::y_ras

Y-direction cosines (yr, ya, ys). Default: (0, 0, -1).

Definition at line 268 of file mri_vol_data.h.

ysize

float MRILIB::MriVolData::ysize

Voxel spacing in Y direction (mm).

Definition at line 265 of file mri_vol_data.h.

z_ras

Eigen::Vector3f MRILIB::MriVolData::z_ras

Z-direction cosines (zr, za, zs). Default: (0, 1, 0).

Definition at line 269 of file mri_vol_data.h.

zsize

float MRILIB::MriVolData::zsize

Voxel spacing in Z direction (mm).

Definition at line 266 of file mri_vol_data.h.

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The documentation for this class was generated from the following files:

• src/libraries/mri/mri_vol_data.h
• src/libraries/mri/mri_vol_data.cpp