vol.read.file.with.affine: Load a volume file and return the data along with the affine...

In fsbrain: Managing and Visualizing Brain Surface Data

Load a volume file and return the data along with the affine transformation.

Description

Supports MGH/MGZ volumes (read with read.fs.mgh) and NIfTI v1 volumes, including oblique ones (read with read.fs.volume.nii, which requires the 'oro.nifti' package). The data array is returned in the storage order of the file, i.e., it is not reoriented, and the returned affine maps 0-based voxel indices (column, row, slice) to world coordinates. This is the convention used by the NIfTI sform and by mghheader.vox2ras.

Usage

vol.read.file.with.affine(filepath)

Arguments

filepath

character string, the path to an .mgz, .mgh, .nii or .nii.gz file.

Value

named list with entries: 'data' (numeric array, 3D or 4D), 'affine' (4x4 numeric matrix), 'filepath' (character string), 'file_format' (character string, either 'mgh' or 'nifti'), and 'frames' (integer, the number of volumes in a 4D file).

Note

If the header of an MGH/MGZ file does not contain a valid vox2ras matrix (ras_good_flag is 0), the surface RAS convention vox2ras_tkr is used for conformed volumes (dimension 256x256x256) and a warning is emitted. For NIfTI files without a valid sform/qform, an error is raised, as the coordinate space is unknown in that case.

fsbrain documentation built on Sept. 27, 2026, 1:07 a.m.