fsbrain (version 0.4.2)

volvis.voxels: Voxel-based visualization of volume mask at surface RAS positions.

Description

Plots a 3D box at every *foreground* voxel in the given volume. All voxels which do not have their intensity value set to `NA` are considered *foreground* voxels. The locations at which to plot the voxels is computed from the voxel CRS indices using the FreeSurfer vox2ras_tkr matrix. This means that the position of the rendered data fits to the surface coordinates (in files like `surf/lh.white`), and that you can call this function while an active surface rendering window is open (e.g., from calling vis.subject.morph.native), to superimpose the surface and volume data. **On coloring the voxels** (using *rgl materials*): Note that you can call this function several times for the active plot, and color the voxels differently by passing different material properties in each call. Alternatively, check the `voxelcol` parameter.

Usage

volvis.voxels(volume, render_every = 1, voxelcol = NULL, ...)

Arguments

volume

numeric 3d array, voxels which should not be plotted must have value `NA`. Take care not to plot too many.

render_every

integer, how many to skip before rendering the next one (to improve performance and/or see deeper structures). Use higher values to see a less dense representation of your data that usually still allows you to see the general shape, but at lower computational burden. Set to 1 to render every (foreground) voxel.

voxelcol

character string or a *voxel coloring*. A *voxel coloring* can be specified in three ways: 1) the string 'from_intensity' will compute colors based on the intensity values of the foreground voxels in the volume, applying normalization of the intensity values if needed. 2) an array of RGB color strings: will be used to retrieve the colors for all foreground vertices, at their CRS indices. 3) A vector with length identical to the number of foreground voxels in the volume: will be applied directly. Obvisouly, you should not pass a color material parameter (see `...`) when using this.

...

material properties, passed to triangles3d. Example: color = "#0000ff", lit=FALSE.

Examples

# NOT RUN {
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   brain = subject.volume(subjects_dir, 'subject1', 'brain');
   # Plot all voxels of the brain:
   brain[which(brain==0L, arr.ind = TRUE)] = NA;  # mark background
   brain = vol.hull(brain); # remove inner triangles
   volvis.voxels(brain);
# }
# NOT RUN {
# }