vis.subject.annot: Visualize an annotation for a subject.

In dfsp-spirit/nitools: Managing and Visualizing Brain Surface Data

Visualize an annotation for a subject.

Description

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.spheres(), 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.subject.label(), vis.subject.morph.native(), vis.subject.morph.standard(), vis.subject.pre(), vis.symmetric.data.on.subject(), vislayout.from.coloredmeshes()

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

Examples

## Not run: 
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   vis.subject.annot(subjects_dir, 'subject1', 'aparc', 'both');

## End(Not run)

dfsp-spirit/nitools documentation built on Jan. 26, 2024, 8:24 p.m.