Create brain atlas from label files — create_cortical_from

Build an atlas from individual FreeSurfer .label files rather than a complete annotation. Each label file defines a single region by listing which surface vertices belong to it.

The function detects hemisphere from filename prefixes (lh. or rh.) and derives region names from the rest of the filename.

Usage

create_cortical_from_labels(
  label_files,
  atlas_name = NULL,
  input_lut = NULL,
  output_dir = NULL,
  views = c("lateral", "medial"),
  tolerance = NULL,
  smooth_refinements = NULL,
  cleanup = NULL,
  verbose = get_verbose(),
  skip_existing = NULL
)

Arguments

label_files: Paths to .label files. Each file should follow FreeSurfer naming: {hemi}.{regionname}.label (e.g., lh.motor.label).
atlas_name: Name for the atlas. If NULL, derived from the input filename.
input_lut: Path to a color lookup table (LUT) file, or a data.frame with columns region and colour columns (R, G, B or hex).
output_dir: Directory to store intermediate files (screenshots, masks, contours). Defaults to tempdir().
views: Which views to include: "lateral", "medial", "superior", "inferior".
tolerance: Simplification tolerance for 2D polygons. Higher values produce simpler shapes with fewer vertices (typical range: 0.1–2). Passed to sf::st_simplify(). If not specified, uses options("ggseg.extra.tolerance") or the GGSEG_EXTRA_TOLERANCE environment variable. Default is 1.
smooth_refinements: Number of Chaikin corner-cutting refinements to apply to 2D polygons. Higher values produce smoother region boundaries (typical range: 0–3). 0 disables smoothing. If not specified, uses options("ggseg.extra.smooth_refinements") or the GGSEG_EXTRA_SMOOTH_REFINEMENTS environment variable. Default is 2.
cleanup: Remove intermediate files after atlas creation. If not specified, uses options("ggseg.extra.cleanup") or the GGSEG_EXTRA_CLEANUP environment variable. Default is TRUE.
verbose: Verbosity level: 0 (silent), 1 (standard progress, default), or 2 (debug, includes FreeSurfer output). Logical values are accepted (TRUE = 1, FALSE = 0). If not specified, uses the value from options("ggseg.extra.verbose") or the GGSEG_EXTRA_VERBOSE environment variable.
skip_existing: Skip generating output files that already exist, allowing interrupted atlas creation to resume. If not specified, uses options("ggseg.extra.skip_existing") or the GGSEG_EXTRA_SKIP_EXISTING environment variable. Default is TRUE.

Value

A ggseg_atlas object.

Examples

if (FALSE) { # \dontrun{
labels <- c("lh.region1.label", "lh.region2.label", "rh.region1.label")
atlas <- create_cortical_from_labels(labels)
} # }