Visualize contour of a volume. — volvis.contour • fsbrain

Compute a smoothed surface from the voxel intensities in the given volume and render it. Requires the misc3d package to be installed, which is an optional dependency.

Usage

volvis.contour(volume, level = 80, show = TRUE, frame = 1L, color = "white")

Arguments

volume: a 3D brain volume
level: numeric, intensity threshold for the data. Voxels with intensity value smaller than level will be ignored when creating the contour surface.
show: logical, whether to display the triangles. Defaults to TRUE.
frame: integer, the frame to show in case of a 4D input volume. Can also be the character string 'all' to draw the contents of all frames at once. Useful to plot white matter tracts from DTI data, where each tract is stored in a different frame.
color: the color to use when plotting. Can be a vector of colors when plotting all frames of a 4D image (one color per frame).

Value

the rendered triangles (a Triangles3D instance) with coordinates in surface RAS space if any, NULL otherwise. This will be a list if you pass a 4D volume and select 'all' frames.

Examples

if (FALSE) { # \dontrun{
   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:
   volvis.contour(brain);
} # }