Generate 3D mesh surface from volume data — mesh_from

This function is soft-deprecated. Please use vcg_mesh_volume, vcg_uniform_remesh, and vcg_smooth_explicit or vcg_smooth_implicit.

Usage

mesh_from_volume(
  volume,
  output_format = c("rgl", "freesurfer"),
  IJK2RAS = NULL,
  threshold = 0,
  verbose = TRUE,
  remesh = TRUE,
  remesh_voxel_size = 1,
  remesh_multisample = TRUE,
  remesh_automerge = TRUE,
  smooth = FALSE,
  smooth_lambda = 10,
  smooth_delta = 20,
  smooth_method = "surfPreserveLaplace"
)

Arguments

volume: 3-dimensional volume array
output_format: resulting data format, choices are 'rgl' and 'freesurfer'
IJK2RAS: volume 'IJK' (zero-indexed coordinate index) to 'tkrRAS' transform, default is automatically determined
threshold: threshold used to create volume mask; the surface will be created to fit the mask boundaries
verbose: whether to verbose the progress
remesh: whether to re-sample the mesh using vcg_uniform_remesh
remesh_voxel_size, remesh_multisample, remesh_automerge: see arguments in vcg_uniform_remesh
smooth: whether to smooth the mesh via vcg_smooth_explicit
smooth_lambda, smooth_delta, smooth_method: see vcg_smooth_explicit

Value

A 'mesh3d' surface if output_format is 'rgl', or 'fs.surface' surface otherwise.

Examples



volume <- array(0, dim = c(8,8,8))
volume[4:5, 4:5, 4:5] <- 1

graphics::image(x = volume[4,,])


# you can use rgl::wire3d(mesh) to visualize the mesh
mesh <- mesh_from_volume(volume, verbose = FALSE)