mri_mgh_io.h File Reference

MriMghIO class declaration. More...

#include "mri_global.h"
#include "mri_vol_data.h"
#include <QString>
#include <QVector>

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Classes
class	MRILIB::MriMghIO
	FreeSurfer MGH/MGZ file reader. More...

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

Detailed Description

MriMghIO class declaration.

Author

Christoph Dinh chris.nosp@m.toph.nosp@m..dinh.nosp@m.@mne.nosp@m.-cpp..nosp@m.org

Since

2.0.0

Date

February, 2026

LICENSE

Copyright (C) 2026, Christoph Dinh. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
• Neither the name of MNE-CPP authors nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

      Reader for FreeSurfer MGH/MGZ (gzip-compressed MGH) volume files.

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

      MGH Header Layout (all big-endian, total 284 bytes):

      Offset  Size  Field
      ------  ----  -----
         0      4   version (int32) — must be 1
         4      4   width (int32) — first image dimension
         8      4   height (int32) — second image dimension
        12      4   depth (int32) — third image dimension
        16      4   nframes (int32) — number of frames
        20      4   type (int32) — voxel data type (0=uchar, 1=int, 3=float, 4=short)
        24      4   dof (int32) — degrees of freedom
        28      2   goodRASflag (int16) — if > 0 the following fields are valid
        30     12   spacingX, spacingY, spacingZ (3×float32) — voxel sizes in mm
        42     36   direction cosines: xr,xa,xs, yr,ya,ys, zr,za,zs (9×float32)
        78     12   c_ras: cr, ca, cs (3×float32) — center RAS coordinates
        90    194   unused (padding to byte 284)

      Image Data (starting at byte 284):
        width × height × depth × nframes × sizeof(type) bytes
        Stored in column-major (Fortran) order: x varies fastest.

      Footer (after image data, optional):
        Scan parameters: TR (float32), flipAngle (float32), TE (float32),
        TI (float32), FoV (float32)
        Tags: type(int32) + length(int32/int64) + data
          TAG_OLD_SURF_GEOM (20): old surface geometry, length is int32
          TAG_OLD_MGH_XFORM (30): old transform, length is int32
          TAG_MGH_XFORM (31): path to talairach.xfm file, length is int64

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

Definition in file mri_mgh_io.h.