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(
  subjects_dir,
  vis_subject_id,
  verts_lh = NULL,
  verts_rh = NULL,
  surface = "white",
  views = c("t4"),
  rgloptions = rglo(),
  rglactions = list(),
  color_bg = "#FEFEFE",
  color_verts_lh = "#FF0000",
  color_verts_rh = "#FF4500",
  k = 0L
)

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'.

verts_lh

integer vector, the indices of left hemisphere vertices.

verts_rh

integer vector, the indices of right hemisphere vertices.

surface

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

views

list of strings. Valid entries include: 'si': single interactive view. 't4': tiled view showing the brain from 4 angles. 't9': tiled view showing the brain from 9 angles.

rgloptions

option list passed to par3d. Example: rgloptions = list("windowRect"=c(50,50,1000,1000)).

rglactions

named list. A list in which the names are from a set of pre-defined actions. The values can be used to specify parameters for the action. The following example clips outliers in the data before plotting and writes a screenshot in PNG format: rglactions = list("snapshot_png"="~/fsbrain.png", "clip_data"=c(0.05, 0.95)). See rglactions.

color_bg

background color.

color_verts_lh

vector of colors to visualize on the left hemisphere surface. Length must match number of vertices in 'verts_lh', or be a single color.

color_verts_rh

vector of colors to visualize on the right hemisphere surface. Length must match number of vertices in 'verts_rh', or be a single color.

k

integer, radius to extend neighborhood (for better visibility).

Value

list of coloredmeshes. The coloredmeshes used for the visualization.

See also

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

Examples

if (FALSE) { # \dontrun{
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   highlight.vertices.on.subject(subjects_dir, 'subject1',
     verts_lh=c(5000, 100000), verts_rh=c(300, 66666), views="si");
} # }