Create surface mesh from 3D-array

Create surface from 3D-array using marching cubes algorithm

Usage

vcg_isosurface(
  volume,
  threshold_lb = 0,
  threshold_ub = NA,
  vox_to_ras = diag(c(-1, -1, 1, 1))
)

Arguments

volume

a volume or a mask volume

threshold_lb

lower-bound threshold for creating the surface; default is 0

threshold_ub

upper-bound threshold for creating the surface; default is NA (no upper-bound)

vox_to_ras

a 4x4 'affine' transform matrix indicating the 'voxel'-to-world transform.

Value

A triangular mesh of class 'mesh3d'

Details

The surface is extracted from the binary mask of the 'voxels' between the thresholds, so it runs between the centers of the 'voxels' inside and outside the mask (0.001 'voxel' outside the midpoint). It is closed, without cracks: the mask is padded with empty 'voxels', so the surface also closes where the mask reaches the border of the array, and 'voxels' that share only an edge are always joined.

Examples

if(is_not_cran()) {

library(ravetools)
data("left_hippocampus_mask")

mesh <- vcg_isosurface(left_hippocampus_mask)


rgl_view({

  rgl_call("mfrow3d", 1, 2)

  rgl_call("title3d", "Direct ISOSurface")
  rgl_call("shade3d", mesh, col = 2)

  rgl_call("next3d")
  rgl_call("title3d", "ISOSurface + Implicit Smooth")

  rgl_call("shade3d",
           vcg_smooth_implicit(mesh, degree = 2),
           col = 3)
})

}
#> Package `rgl` is not installed. Please install `rgl` to use this function.
#> Error in loadNamespace(name): there is no package called ‘rgl’