trackvis.affine.to.rasmm: Compute the affine that maps TrackVis coordinates to RAS+ mm.

In freesurferformats: Read and Write 'FreeSurfer' Neuroimaging File Formats

Compute the affine that maps TrackVis coordinates to RAS+ mm.

Description

Computes the affine that turns the streamlines stored in a TRK file into RAS+ mm coordinates in which a coordinate of (0,0,0) is the center of the first voxel, which is the convention used by 'nibabel', DIPY and the TRX format. The stored streamlines refer to the voxel corners and are in "voxelmm" space, so this combines the stored matrix with the voxel sizes, the half-voxel offset, and the orientation stored in the voxel_order header field.

Usage

trackvis.affine.to.rasmm(header)

Arguments

header

named list, the header of a TRK file as returned by read.dti.trk.header.

Value

a 4x4 numeric matrix.

Note

The TrackVis specification assumes that the stored streamlines are in mm and that the stored matrix maps them to RAS, which means the matrix has to be corrected whenever the voxels are not 1 mm^3. DSI Studio writes files that do not need the half-voxel shift, which is what the shift_origin parameter of read.dti.trk controls.

freesurferformats documentation built on Sept. 25, 2026, 1:07 a.m.