vol.tkreg.affine: Transform a volume affine matrix into the FreeSurfer...

In fsbrain: Managing and Visualizing Brain Surface Data

Transform a volume affine matrix into the FreeSurfer tkregister convention.

Description

FreeSurfer stores brain surfaces (and all surface-based data) in the surface RAS coordinate system, which is also called the tkregister or tkreg space: the RAS coordinate (0, 0, 0) is at the center of the field of view of the volume. The transformation from voxel indices to this space is not the transformation stored in the header of the volume: a volume can have a center-of-RAS offset (cras), which is preserved by FreeSurfer in the header but ignored by the surface-based tools (this is the difference between the --vox2ras and --vox2ras-tkr options of mri_vol2surf).

This function takes the header transformation matrix of a volume and returns the corresponding tkregister matrix, i.e., the same direction cosines and voxel sizes, but with the translation replaced so that the center of the volume is at RAS (0, 0, 0). For a conformed FreeSurfer volume (256x256x256 voxels of 1 mm), the result is identical to vox2ras_tkr.

Usage

vol.tkreg.affine(affine, dims)

Arguments

affine	numeric 4x4 matrix, the transformation matrix from the volume header (maps 0-based voxel indices to world coordinates).
dims	integer vector of length 3 or more, the dimensions of the volume (dim(volume_data)).

Value

numeric 4x4 matrix, the tkregister transformation matrix.

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