ieegio (version 0.0.9)

io-trk: Read or write 'TCK' streamlines

Description

Low-level functions; for high-level functions, please use read_streamlines or as_ieegio_streamlines instead.

Low-level functions, supports compressed files; for high-level functions, please use read_streamlines or as_ieegio_streamlines instead.

Usage

io_read_tck(file)
io_write_tck(
  x,
  con,
  datatype = c("Float32LE", "Float32BE", "Float64LE", "Float64BE")
)
io_read_trk(file, half_voxel_offset = TRUE)
io_write_trk(x, con, half_voxel_offset = NA)

Value

io_read_tck returns a ieegio streamline object, io_write_tck returns the connection or file path.

io_read_trk returns an imaging-streamlines

instance.

Arguments

file, con

file path to the streamline file

x

imaging-streamlines instance

datatype

data storage type to write, default is 'Float32LE', 4-byte little 'endian' float; other choices are 'Float32BE', 'Float64LE', and 'Float64BE'

half_voxel_offset

whether to add 0.5 millimeter shift on each side, default is TRUE. See 'Details' for explanation.

Details

'TRK' gains popularity due to its ability to store streamline attributes. However, this file format suffer from ambiguous definition in the initial 'TrackVis' implementation. Typically in a medical image file, there might exists a 4-by-4 matrix that maps the volume indices to the corresponding anatomical right-anterior-superior 'RAS' locations. However, the original definition of 'TRK' does not have this. Since version 2, 'TRK' introduced such matrix, but it was interpreted differently. Instead of the volume index space, the source space is conformed 1 millimeter space, with the origin at the first 'voxel' corner instead of the center. Therefore there is a 0.5 mm shift at each direction, and half_voxel_offset is designed to offset this shift.

What has made this issue complicated was that some software, such as 'DSI-studio', seemed to ignore that offset when converting from their own format to the 'TRK' format. If the file is generated in such way, please set half_voxel_offset=FALSE to turn off the offset correction. We always recommend that user store data in 'TCK' format.

Examples

# run `ieegio_sample_data("streamlines/CNVII_R.tck")` to
# download sample data

if( ieegio_sample_data("streamlines/CNVII_R.tck", test = TRUE) ) {

  path <- ieegio_sample_data("streamlines/CNVII_R.tck")

  # Read
  streamlines <- io_read_tck(path)

  plot(streamlines)

  # write
  tfile <- tempfile(fileext = ".tck")
  io_write_tck(streamlines, tfile, datatype = streamlines$header$datatype)

  # verify two files are identical
  digest::digest(file = tfile) == digest::digest(file = path)


  unlink(tfile)

}





# This example uses sample data, run
# `ieegio_sample_data("streamlines/CNVII_R.trk")` to download

if( ieegio_sample_data("streamlines/CNVII_R.trk", test = TRUE) ) {

  path <- ieegio_sample_data("streamlines/CNVII_R.trk")
  tfile <- tempfile(fileext = ".trk")

  # read
  x <- io_read_trk(path)

  # write
  io_write_trk(x, tfile)

  # compare two files
  file.size(path) == file.size(tfile)

  src_raw <- readBin(path, "raw", n = file.size(path))
  dst_raw <- readBin(tfile, "raw", n = file.size(tfile))

  equal_raw <- src_raw == dst_raw

  # Some reserved information are removed
  all(equal_raw[-c(945:947)])

  unlink(tfile)

}