freesurferformats (version 1.1.0)

read.fs.tracts.vtk: 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)

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.

Arguments

filepath

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

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))
))