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Public Member Functions | Public Attributes | List of all members
MRILIB::MriVolData Class Reference

MRI volume data from FreeSurfer MGH/MGZ file. 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

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

MRI volume data from FreeSurfer MGH/MGZ file.

Holds a complete MRI volume loaded from a FreeSurfer MGH/MGZ file.

This class encapsulates all header geometry, coordinate transforms, scan parameters, and voxel data that describe a 3D MRI volume.

Based on the FreeSurfer MGH format specification: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat

Header structure (all big-endian):

  • version (int32): current value is 1
  • width (int32): first dimension (fastest-varying)
  • height (int32): second dimension
  • depth (int32): third dimension (slowest)
  • nframes (int32): number of scalar components per voxel
  • type (int32): voxel data type (MRI_UCHAR=0, MRI_INT=1, MRI_FLOAT=3, MRI_SHORT=4)
  • dof (int32): degrees of freedom
  • goodRASflag (int16): if true, direction cosines follow
  • spacingX/Y/Z (float32): voxel sizes in mm
  • Mdc (9×float32): direction cosine matrix (column-major)
  • c_ras (3×float32): center RAS coordinates
  • (padding to byte 284)

Image data starts at byte 284.

Footer (after data): optional scan parameters (TR, FlipAngle, TE, TI, FoV) and tags (Talairach transform path, provenance info).

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

Definition at line 148 of file mri_vol_data.h.

Constructor & Destructor Documentation

◆ MriVolData()

MriVolData::MriVolData ( )

Default constructor.

Definition at line 55 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-surface-RAS transform in meters.

Definition at line 129 of file mri_vol_data.cpp.

◆ dims()

QVector< int > MRILIB::MriVolData::dims ( ) const
inline
Returns
Volume dimensions as {dimX, dimY, dimZ}.

Definition at line 201 of file mri_vol_data.h.

◆ dimX()

int MRILIB::MriVolData::dimX ( ) const
inline
Returns
First (x) dimension — fastest-varying axis.

Definition at line 183 of file mri_vol_data.h.

◆ dimY()

int MRILIB::MriVolData::dimY ( ) const
inline
Returns
Second (y) dimension.

Definition at line 189 of file mri_vol_data.h.

◆ dimZ()

int MRILIB::MriVolData::dimZ ( ) const
inline
Returns
Third (z) dimension — slowest-varying axis.

Definition at line 195 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 81 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]pathPath to the .mgh or .mgz file.
Returns
True on success, false on error.

Definition at line 88 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 96 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 248 of file mri_vol_data.h.

◆ depth

int MRILIB::MriVolData::depth

Third dimension (slowest).

Definition at line 237 of file mri_vol_data.h.

◆ dof

int MRILIB::MriVolData::dof

Degrees of freedom.

Definition at line 240 of file mri_vol_data.h.

◆ fileName

QString MRILIB::MriVolData::fileName

Name of the source file.

Definition at line 233 of file mri_vol_data.h.

◆ flipAngle

float MRILIB::MriVolData::flipAngle

Flip angle (radians).

Definition at line 261 of file mri_vol_data.h.

◆ FoV

float MRILIB::MriVolData::FoV

Field of view (unreliable per FreeSurfer docs).

Definition at line 264 of file mri_vol_data.h.

◆ height

int MRILIB::MriVolData::height

Second dimension.

Definition at line 236 of file mri_vol_data.h.

◆ nframes

int MRILIB::MriVolData::nframes

Number of frames (scalar components per voxel).

Definition at line 238 of file mri_vol_data.h.

◆ rasGood

bool MRILIB::MriVolData::rasGood

Whether the direction cosines in the header are valid.

Definition at line 241 of file mri_vol_data.h.

◆ slices

QVector<MriSlice> MRILIB::MriVolData::slices

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

Definition at line 276 of file mri_vol_data.h.

◆ talairachXfmPath

QString MRILIB::MriVolData::talairachXfmPath

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

Definition at line 270 of file mri_vol_data.h.

◆ TE

float MRILIB::MriVolData::TE

Echo time (ms).

Definition at line 262 of file mri_vol_data.h.

◆ TI

float MRILIB::MriVolData::TI

Inversion time (ms).

Definition at line 263 of file mri_vol_data.h.

◆ TR

float MRILIB::MriVolData::TR

Repetition time (ms).

Definition at line 260 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 239 of file mri_vol_data.h.

◆ version

int MRILIB::MriVolData::version

MGH format version (should be 1).

Definition at line 234 of file mri_vol_data.h.

◆ voxelSurfRasT

FIFFLIB::FiffCoordTrans MRILIB::MriVolData::voxelSurfRasT

Voxel -> surface RAS (MRI) transform.

Definition at line 254 of file mri_vol_data.h.

◆ width

int MRILIB::MriVolData::width

First dimension of the image buffer (fastest).

Definition at line 235 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 245 of file mri_vol_data.h.

◆ xsize

float MRILIB::MriVolData::xsize

Voxel spacing in X direction (mm).

Definition at line 242 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 246 of file mri_vol_data.h.

◆ ysize

float MRILIB::MriVolData::ysize

Voxel spacing in Y direction (mm).

Definition at line 243 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 247 of file mri_vol_data.h.

◆ zsize

float MRILIB::MriVolData::zsize

Voxel spacing in Z direction (mm).

Definition at line 244 of file mri_vol_data.h.

The documentation for this class was generated from the following files:
Generated on for MNE-CPP by doxygen 1.16.1