read.dti.trk: Read fiber tracks from Diffusion Toolkit in trk format.

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

Read fiber tracks from Diffusion Toolkit in trk format.

Description

Read fiber tracks from Diffusion Toolkit in trk format.

Usage

read.dti.trk(filepath, shift_origin = TRUE)

Arguments

filepath

character string, path to file in trk format.

shift_origin

logical, whether to apply the half-voxel origin shift when computing the corrected vox2ras matrix. The TRK format stores a matrix that maps to the voxel corner, not the voxel center (as is the NIfTI convention). Set to 'TRUE' (the default) to compute the corrected 'vox2ras' that maps to voxel centers, as used by TrackVis. Set to 'FALSE' if the file was written by DSI Studio, which does not apply this shift. See the notes for details.

Value

named list, the parsed file data. The naming of the variables follows the spec at http://trackvis.org/docs/?subsect=fileformat. The returned header will contain the field 'vox2ras' (the raw matrix stored in the TRK file, mapping from mm space to RAS) and, if 'shift_origin' is 'TRUE', the additional field 'vox2ras_corrected' (the computed matrix mapping from voxel indices to voxel center RAS coordinates).

Note

The 4x4 matrix stored in TRK files (labeled 'vox_to_ras' in the spec) is actually a transformation from **mm** space to RAS, not from voxel space to RAS. The TRK format was designed by TrackVis with the assumption that voxels are 1 mm^3, and that coordinates refer to voxel corners rather than centers. To obtain the actual vox2ras matrix (voxel center in RAS), the raw matrix must be combined with a voxel-size scaling and a half-voxel offset correction: 'vox2ras_corrected = mm2ras

Examples

## Not run: 
trk = read.dti.trk("~/simple.trk");
trk2 = read.dti.trk("~/standard.trk");
trk3 = read.dti.trk("~/complex_big_endian.trk");

## End(Not run)

freesurferformats documentation built on July 8, 2026, 5:08 p.m.