Highlight vertices given by index on a subject's meshes by coloring faces.

Highlight vertices given by index on a subject's meshes by coloring faces.

Usage

highlight.vertices.on.subject.spheres(
  subjects_dir,
  vis_subject_id,
  vertices,
  surface = "white",
  patch_size = 25,
  show_patch = TRUE,
  style = "glass2",
  export_img = NULL,
  sphere_colors = c("#FF0000"),
  sphere_radius = 3,
  ...
)

Arguments

subjects_dir

string. The FreeSurfer SUBJECTS_DIR, i.e., a directory containing the data for all your subjects, each in a subdir named after the subject identifier.

vis_subject_id

string. The subject identifier from which to obtain the surface for data visualization. Example: 'fsaverage'.

vertices

positive integer vector, the vertex indices over both hemispheres. Alternative to using verts_lh and verts_rh parameters, only one of them must be used at once.

surface

string. The display surface. E.g., "white", "pial", or "inflated". Defaults to "white".

patch_size

double, geodesic radius in which to draw a patch on the mesh around the verts. Pass NULL to disable.

show_patch

logical (or a vector with one logical value per entry in 'vertices'), whether to show colored geodesic patches at the highlighted vertices.

style

character string or rgl rendering style, see get.rglstyle.

export_img

character string, the path to the output image if you want to export a high-quality image, NULL if you want live visualization instead.

sphere_colors

the sphere colors like '#FF0000', can be a single one for all or one per sphere

sphere_radius

double, a single radius for all spheres

...

extra parameters passed on to vis.data.on.subject. Use this to set a custom colormap etc.

Value

list of coloredmeshes. The coloredmeshes used for the visualization. If export_img is set, the export return value is returned instead.

Note

If no patches are visualized, the color used for the brain can be set with options("fsbrain.brain_na_color"="#FF0000").

See also

Other visualization functions: highlight.vertices.on.subject(), vis.color.on.subject(), vis.data.on.fsaverage(), vis.data.on.subject(), vis.labeldata.on.subject(), vis.mask.on.subject(), vis.region.values.on.subject(), vis.rglwidget(), vis.subject.annot(), vis.subject.label(), vis.subject.morph.native(), vis.subject.morph.standard(), vis.subject.pre(), vis.symmetric.data.on.subject(), vis.volume.on.surface(), vislayout.from.coloredmeshes()

Other surface visualization functions: highlight.vertices.on.subject(), vis.color.on.subject()

Examples

if (FALSE) { # \dontrun{
   fsbrain::download_fsaverage(T);
   subjects_dir = fsaverage.path();
   mkco = list('colFn'=viridis::viridis, 'n'=300);
   # Ex.1: highlight with patches and custom colormap:
   highlight.vertices.on.subject.spheres(subjects_dir, 'fsaverage',
     vertices=c(300, 5000, 100000), makecmap_options = mkco);
   # Ex.2: show patches on some (red) vertices, not on blue ones:
   highlight.vertices.on.subject.spheres(subjects_dir, 'fsaverage',
     vertices=c(300, 5000, 100000, 300000), show_patch = c(T,F,T,F),
     sphere_colors = c("red", "blue", "red", "blue"));
} # }