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Create brain atlas from label files

Source: R/atlas_cortical.R
create_cortical_from_labels.Rd

[Experimental]

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,
  input_lut = NULL,
  atlas_name = 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).

input_lut

Path to a color lookup table (LUT) file, or a data.frame with a region column (or a FreeSurfer-style label column) plus colour columns (R, G, B or hex). Rows must be in the same order as the input files.

atlas_name

Name for the atlas. If NULL, derived from the input filename.

output_dir

Directory to store intermediate files (screenshots, masks, contours). Defaults to tempdir().

views

Which views to include: "lateral", "medial", "superior", "inferior".

tolerance

[Deprecated] sf simplification is no longer applied during atlas creation. Use atlas_smooth() on the returned atlas instead. Supplying a value emits a lifecycle warning and is otherwise ignored.

smooth_refinements

[Deprecated] sf-side smoothing is no longer applied during atlas creation. Use atlas_smooth() on the returned atlas instead. Supplying a value emits a lifecycle warning and is otherwise ignored.

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)
} # }