read.fs.tracts.vtk: Read VTK legacy format streamlines as tracts.

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

Read VTK legacy format streamlines as tracts.

Description

Reads streamline (tractography) data from files in the VTK legacy format, i.e. from POLYDATA datasets that contain a LINES section. Both the ASCII and the binary encoding are supported, as are the cell array layouts written by VTK 4.2 and older and by VTK 5.1 and newer. This is the format that Paraview, TrackVis and DSI Studio export streamlines in. Attribute data such as scalar values per point is ignored.

Usage

read.fs.tracts.vtk(filepath)

Arguments

filepath

character string, path to the input file in VTK legacy format.

Value

an fs.tracts instance with the streamlines. Use tracts[[i]] to get the n x 3 coordinate matrix of a single streamline, and fs.tracts.lengths for the number of points of each streamline.

Note

Points that are not part of any streamline are dropped, because the fs.tracts data structure stores the coordinates of the streamlines without gaps. A warning is issued if that happens.

Examples

# The example file was written by VTK and contains 3 streamlines.
# It also has a point that is not part of any streamline, which is dropped with a warning.
tracts_file <- system.file("extdata", "tracts_v51_binary.vtk",
  package = "freesurferformats", mustWork = TRUE
)
tracts <- suppressWarnings(read.fs.tracts.vtk(tracts_file))
cat(sprintf(
  "Read %d streamlines with %d points.\n",
  length(tracts), nrow(fs.tracts.coords(tracts))
))

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