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MriMghIO

Namespace: MRILIB  ·  Library: MRI Library

#include <mri/mri_mgh_io.h>

class MRILIB::MriMghIO

Stateless decoder for FreeSurfer MGH and MGZ volume containers.

Parses the 284-byte big-endian header, decodes the column-major voxel buffer for every supported MRI type (uchar, int, float, short) and reads the optional tag footer (scan parameters, talairach.xfm path) into an MriVolData. .mgz inputs are inflated in-memory through zlib's MAX_WBITS+16 gunzip mode before parsing, so callers never need to know whether they are looking at the compressed or uncompressed variant.

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

Ported from make_mgh_cor_set() in MNE C mne_make_cor_set by Matti Hamalainen.

src/examples/ex_mri/main.cpp
MriVolData mgh;
QVector<FiffCoordTrans> extraTransforms; // e.g. Talairach, if the footer names one
MriMghIO::read(dataDir + "/gradient.mgz", mgh, extraTransforms);
const Matrix4f vox2ras = mgh.computeVox2Ras();        // scanner RAS, metres
const QVector<float> voxels = mgh.voxelDataAsFloat(); // x fastest

Static Methods​

read(mgzFile, volData, additionalTrans, subjectMriDir, verbose)​

Reads a FreeSurfer MGH or MGZ file.

Parses the header geometry (dimensions, voxel sizes, direction cosines, center RAS), reads voxel data into per-slice MriSlice structures, and extracts footer tags including the Talairach .xfm path.

For .mgz files, automatic gzip decompression is performed via zlib.

Parameters:

  • mgzFile : const QString & Path to the .mgz or .mgh file.

  • volData : MriVolData & MriVolData structure to populate.

  • additionalTrans : QVector< FiffCoordTrans > & Surface RAS -> RAS and, if the footer names a talairach.xfm, the Talairach chain of FiffCoordTransSet.

  • subjectMriDir : const QString & Path to subject's mri/ directory (for resolving relative .xfm paths).

  • verbose : bool If true, print progress information.

Returns:

  • bool — True on success, false on error.

Example​

Used in examples​

ex_mri​

MRI library: MGH/MGZ and NIfTI volumes, voxel/RAS transforms, slicing and COR sets.

src/examples/ex_mri/main.cpp, line 92
MriVolData mgh;
QVector<FiffCoordTrans> extraTransforms; // e.g. Talairach, if the footer names one
MriMghIO::read(dataDir + "/gradient.mgz", mgh, extraTransforms);
const Matrix4f vox2ras = mgh.computeVox2Ras();        // scanner RAS, metres
const QVector<float> voxels = mgh.voxelDataAsFloat(); // x fastest
Matrix4f vox2rasMm = vox2ras;
vox2rasMm.block<3, 4>(0, 0) *= 1000.0f;
ok &= expect(mgh.dims() == QVector<int>({6, 5, 4}) && (vox2rasMm - nibabelAffine).cwiseAbs().maxCoeff() < 1e-4f && voxels.size() == 120 && voxels[2 + 6 * (3 + 5 * 1)] == 82.0f,
             "MGZ: 6x5x4 voxels, vox2ras and voxel (2,3,1) = 82 match nibabel");

Authors of this file​