Apply a linear RAS transform to resample a 3D volume

Warps a moving volume onto a reference grid given a 4x4 RAS-to-RAS transform (such as the transform returned by register_volume3d). The transform maps reference (fixed) RAS coordinates to moving RAS coordinates.

This function is superseded by apply_transform3d_volume, which additionally applies deformation fields and whole transform chains, and by apply_transform3d_points for coordinates. It is kept, with unchanged behavior and no warning, for existing code; new code should use apply_transform3d_volume. For a single linear transform the two give identical results (except that apply_transform3d_volume offers no 'bspline' interpolation).

Usage

apply_transform3d(
  volume,
  vox2ras,
  transform,
  reference_dim = dim(volume),
  reference_vox2ras = vox2ras,
  interpolation = c("trilinear", "nearest", "bspline"),
  na_fill = 0
)

Arguments

volume

moving 3D array to resample

vox2ras

the moving volume's voxel-to-RAS 4x4 transform

transform

4x4 RAS-to-RAS transform (fixed to moving)

reference_dim

output dimension (the fixed grid); defaults to dim(volume)

reference_vox2ras

the fixed grid's voxel-to-RAS transform; defaults to vox2ras

interpolation

'trilinear' (default), 'nearest', or 'bspline' (cubic Catmull-Rom)

na_fill

value for out-of-bounds voxels; default 0

Value

The resampled volume on the reference grid, with a 'vox2ras' attribute equal to reference_vox2ras.

See also

apply_transform3d_volume (the replacement), register_volume3d