volvis.contour {fsbrain}

Visualize contour of a volume.

Description

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

## 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:
   volvis.contour(brain);

## End(Not run)