fsbrain (version 0.1.0)

collayer.bg.atlas: Compute atlas or annotation surface color layer.

Description

Compute atlas or annotation surface color layer.

Usage

collayer.bg.atlas(
  subjects_dir,
  subject_id,
  hemi = "both",
  atlas = "aparc",
  grayscale = !outline,
  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 or integer, whether to draw the atlas regions as outlines only. If an integer, it is interpreted as the outline thickness. The value `TRUE` is equivalent to the integer value `1L` and leads to a thin border. The value `2L` will expand the border by 1. If this is active, the surface mesh of the subject must exist.

outline_surface

character string, the surface to load. Only relevant when 'outline' is used.

Value

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

See Also

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

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