freesurferformats (version 1.0.2)

read.dti.trk: 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)

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).

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.

Examples

if (FALSE) {
trk <- read.dti.trk("~/simple.trk")
trk2 <- read.dti.trk("~/standard.trk")
trk3 <- read.dti.trk("~/complex_big_endian.trk")
}