vol.load: Load a volume (from file or memory) and return the data along...

In fsbrain: Managing and Visualizing Brain Surface Data

Load a volume (from file or memory) and return the data along with the affine transformation.

Description

Load a volume (from file or memory) and return the data along with the affine transformation.

Usage

vol.load(volume, default_dir = NULL, affine = NULL, vox2ras = "auto")

Arguments

volume	character string or named list. If a string, either a volume filepath or the name of a volume file without extension. If a named list, an in-memory volume with entries 'data' (numeric 3D or 4D array) and 'affine' (4x4 numeric matrix mapping 0-based voxel indices to world coordinates).
default_dir	character string or NULL, the directory used to resolve volumes specified as names without extension.
affine	numeric 4x4 matrix or NULL. If given, it is used instead of the transformation matrix from the volume header. This is rarely needed, but can help if the header of a volume is missing or wrong. See vox2ras for the interpretation of a volume whose header does not match the surfaces.
vox2ras	character string, how to compute the transformation from voxel indices to world coordinates for the volume: 'auto' (the default) uses vol.tkreg.affine (the FreeSurfer tkregister convention, in which the surfaces are defined) for MGH/MGZ volumes, and the transformation matrix from the file header for NIfTI volumes. 'tkr' forces the tkregister convention, 'header' forces the matrix from the volume header. This corresponds to the --vox2ras-tkr and --vox2ras options of mri_vol2surf. Ignored if affine is given.

Value

named list with entries 'data', 'affine' and 'filepath' (see vol.read.file.with.affine).

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