Compute atlas or annotation surface color layer.

Compute atlas or annotation surface color layer.

Usage

collayer.bg.atlas(
  subjects_dir,
  subject_id,
  hemi = "both",
  atlas = "aparc",
  grayscale = FALSE,
  outline = FALSE,
  outline_surface = "white"
)

Arguments

subjects_dir

character string, the FreeSurfer SUBJECTS_DIR.

subject_id

character string, the subject identifier.

hemi

character string, one of 'lh', 'rh', or 'both'. The latter will merge the data for both hemis into a single vector.

atlas

character string, the atlas name. E.g., "aparc", "aparc.2009s", or "aparc.DKTatlas". Used to construct the name of the annotation file to be loaded.

grayscale

logical, whether to convert the atlas colors to grayscale

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').

outline_surface

character string, the surface to load. Only relevant when 'outline' is used. (In that case the surface mesh is needed to compute the vertices forming the region borders.)

Value

a color layer, i.e., vector of color strings in a hemilist

Note

Using 'outline' mode is quite slow, and increasing the border thickness makes it even slower.

See also

You can plot the return value using vis.color.on.subject.

Other surface color layer: collayer.bg(), collayer.bg.meancurv(), collayer.bg.sulc(), collayer.from.annot(), collayer.from.annotdata(), collayer.from.mask.data(), collayer.from.morphlike.data(), collayers.merge()