Create an fs.transform instance. — fs.transform • freesurferformats

An fs.transform is a linear transformation matrix together with the coordinate spaces that it maps between. It is the common representation that all transformation file format readers and writers in this package return and accept, so that a matrix read from a file always states what its numbers mean: a bare 4x4 matrix does not tell whether it maps voxel indices or world coordinates, in which direction it goes, or whether the voxel indices are zero- or one-based.

The matrix field always maps from the source to the target, i.e., applying it to a coordinate means target_coord = matrix \%*\% c(source_coord, 1), which is the same convention that doapply.transform.mtx uses. The inverse of the transformation is never stored, see invert.fs.transform.

Usage

fs.transform(
  matrix,
  space_in = NA_character_,
  space_out = NA_character_,
  voxel_base = NA_integer_,
  src = NULL,
  dst = NULL,
  format = NA_character_,
  source = NULL,
  type = NULL,
  ...
)

Arguments

matrix: 4x4 numerical matrix, the transformation matrix. Required.
space_in: character string, the kind of coordinates the matrix maps from, one of 'voxel' (voxel indices of a volume), 'ras' (world coordinates, right-anterior-superior in millimeters) or 'lps' (world coordinates, left-posterior-superior in millimeters, used by ITK and ITK-based tools like ANTs). Use NA if the file did not state the space.
space_out: character string, the kind of coordinates the matrix maps to, see space_in.
voxel_base: integer, either 0 or 1. The index of the first voxel in the coordinates the matrix consumes and produces, i.e. 1 for the convention used by FreeSurfer and tkregister, and 0 for the one used by NIfTI, FSL and ITK. Must be NA unless space_in or space_out is 'voxel', since the value is meaningless for world coordinates.
src: NULL or named list, the volume or template that the matrix maps from. See volume.descriptor.
dst: NULL or named list, the volume or template that the matrix maps to.
format: character string, the file format the transform was read from, one of 'lta', 'dat', 'xfm' or 'fslmat'. Use NA if the transform was not read from a file.
source: NULL or character string, the path of the file the transform was read from.
type: NULL or character string, the transform type as stated by the file format (e.g. 'Linear' for an xfm file, or the numeric LTA type as a string). This is format-specific metadata and is not interpreted by the package.
...: additional named fields to store in the transform, e.g. the parsed header of the file it was read from. They are not validated and are preserved for formats that carry extra metadata.

Value

an fs.transform instance.