volume.descriptor: Describe a volume for an fs.transform.

Description

Transformation files often record the geometry of the volumes they relate, either completely (an LTA file stores the voxel dimensions, the voxel sizes and the voxel-to-RAS direction vectors of both volumes) or not at all. This helper turns that information into the src and dst descriptors of an fs.transform.

The frame entry states which RAS coordinates the vox2ras matrix produces: 'scanner' means that the matrix is used as given (this is what an LTA file records), and 'tkreg' means FreeSurfer tkregister coordinates, which are RAS coordinates with an identity rotation and the origin at the center of the volume. A descriptor may be partial, e.g. when only the target is known to be in tkregister space.

Usage

volume.descriptor(
  path = NULL,
  dim = NULL,
  voxelsize = NULL,
  xras = NULL,
  yras = NULL,
  zras = NULL,
  cras = NULL,
  vox2ras = NULL,
  frame = "scanner",
  valid = NULL
)

Value

NULL if no information was given, a named list describing the volume otherwise.

Arguments

path: NULL or character string, the file name of the volume as recorded in the transform file.
dim: NULL or integer vector of length 3, the volume dimensions (number of voxels along each axis).
voxelsize: NULL or numerical vector of length 3, the size of a voxel in mm along each axis.
xras: NULL or numerical vector of length 3, the RAS direction of the first voxel axis, scaled by the voxel size. This is the 'xras' entry of the volume info section of an LTA file.
yras: NULL or numerical vector of length 3, the RAS direction of the second voxel axis, scaled by the voxel size.
zras: NULL or numerical vector of length 3, the RAS direction of the third voxel axis, scaled by the voxel size.
cras: NULL or numerical vector of length 3, the RAS coordinates of the center of the volume, i.e. of voxel index dim/2. This is not the RAS coordinate of the first voxel, and using it as the translation column of a voxel-to-RAS matrix is an error of half the field of view. The 'cras' entry of the volume info section of an LTA file follows this convention, as verified against mri_info --cras.
vox2ras: NULL or 4x4 numerical matrix, the transformation from voxel indices to RAS coordinates. If not given but dim, xras, yras, zras and cras are, the matrix is computed from them in the convention that mghheader.vox2ras implements for MGH headers: zero-based voxel indices and the origin at cras - Mdc_scaled * (dim/2). Verified against mri_info --vox2ras on a real volume.
frame: character string, either 'scanner', 'tkreg' or 'fsl', see the description.
valid: NULL or integer, the 'valid' flag of the volume info section of an LTA file, which states whether the recorded geometry could be used by FreeSurfer.