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

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

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 = 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.meancurv(), collayer.bg.sulc(), collayer.bg(), collayer.from.annotdata(), collayer.from.annot(), collayer.from.mask.data(), collayer.from.morphlike.data(), collayers.merge()

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