freesurferformats (version 1.1.0)

write.dti.trk: Write tracks to a file in TrackVis TRK format.

Description

Writes streamlines in the TRK format described at http://trackvis.org/docs/?subsect=fileformat. The output is read by TrackVis, by DSI Studio and by read.dti.trk.

Usage

write.dti.trk(
  tracts,
  filepath,
  header = NULL,
  coords_space = NULL,
  endian = "little",
  gzip = NULL
)

Value

the file path, invisibly.

Arguments

tracts

the tracks to write, either an fs.tracts instance as returned in the tracks entry of read.dti.trk, or a list of numeric matrices with 3 columns, or a single such matrix. Per-point scalars and per-track properties are written if the input is an fs.tracts instance that has them.

filepath

character string, the path of the file to write.

header

named list or NULL, the header of the file the tracks were read from, whose metadata (voxel sizes, dimensions, the voxel-to-RAS matrix, the voxel order, and the scalars and properties of the file) is reused. If NULL, a minimal header is written that describes coordinates in 1 mm isotropic voxels with an identity voxel-to-RAS matrix, which is the case that needs no coordinate correction at all.

coords_space

character string or NULL, the coordinate system the tracks are in, either 'native' (the coordinates are written as they are) or 'ras' (the coordinates are RAS+ mm and are transformed back to the space used in the file, which is what 'nibabel' does when saving). If NULL (the default), the value stored in header$coords_space is used when present, and 'native' otherwise. This makes a read-write round trip with coords = 'ras' work without any further arguments.

endian

character string, 'little' (the default) or 'big'. TrackVis writes little endian files, big endian support is for reading files written on old big endian systems.

gzip

logical or NULL, whether to gzip-compress the output. If NULL (the default), the file is compressed when the file name ends in '.gz'. Note that the TrackVis tools and MRtrix do not read compressed track files, so this is useful for archiving and for passing the file back to read.dti.trk, but not for exchanging it with other software.

Examples

if (FALSE) {
trk <- read.dti.trk("brain.trk");
write.dti.trk(trk$tracks, "copy.trk", header = trk$header);

# Write RAS coordinates back to a file that uses voxelmm space:
trk_ras <- read.dti.trk("brain.trk", coords = "ras");
write.dti.trk(trk_ras$tracks, "copy.trk", header = trk_ras$header, coords_space = "ras");
}