Visualize an annotation for a subject.

Creates a surface mesh, loads the colors from the annotation, and renders the resulting colored mesh in an interactive window. If hemi is 'both', the data is rendered for the whole brain.

Usage

vis.subject.annot(
  subjects_dir,
  subject_id,
  atlas,
  hemi = "both",
  surface = "white",
  views = c("t4"),
  rgloptions = rglo(),
  rglactions = list(),
  outline = FALSE,
  style = "default"
)

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.

subject_id

string. The subject identifier.

atlas

string. The atlas name. E.g., "aparc", "aparc.2009s", or "aparc.DKTatlas". Used to construct the name of the annotation file to be loaded. Can also be a hemilist of already loaded annotations.

hemi

string, one of 'lh', 'rh', or 'both'. The hemisphere name. Used to construct the names of the label data files to be loaded.

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.

outline

logical, whether to draw an outline only instead of filling the regions. Defaults to FALSE. Instead of passing TRUE, one can also pass a list of extra parameters to pass to annot.outline, e.g., outline=list('outline_color'='#000000'). Using this increases computation time dramatically, sorry for the performance.

style

character string, a rendering style, e.g., 'default', 'shiny' or 'semitransparent'.

Value

list of coloredmeshes. The coloredmeshes used for the visualization.

See also

Other visualization functions: highlight.vertices.on.subject(), 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.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 region-based visualization functions: vis.region.values.on.subject()

Examples

if (FALSE) { # \dontrun{
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   vis.subject.annot(subjects_dir, 'subject1', 'aparc', 'both');
} # }