Create cerebellar atlas from volume segmentation

Creates a cerebellar atlas from a NIfTI segmentation volume. Uses the bundled SUIT 3D surface for volume-to-surface sampling and the SUIT flatmap for 2D polygon generation. Per-region 3D meshes are tessellated from the volume for 3D rendering.

Usage

create_cerebellar_from_volume(
  input_volume = NULL,
  input_lut = NULL,
  atlas_name = NULL,
  output_dir = NULL,
  decimate = 0.5,
  tolerance = NULL,
  smooth_refinements = NULL,
  cleanup = NULL,
  verbose = get_verbose(),
  skip_existing = NULL,
  volume = lifecycle::deprecated()
)

Arguments

input_volume

Path to a cerebellar segmentation volume (NIfTI).

input_lut

Optional path to a colour lookup table file, or a data.frame with columns idx, label, and optionally R, G, B. If NULL, labels are auto-generated from volume values.

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().

decimate

Mesh decimation factor between 0 and 1. Reduces the number of faces in 3D meshes using quadric edge decimation (via Rvcg::vcgQEdecim()). A value of 0.5 reduces faces by 50%. Set to NULL to skip decimation. Requires the Rvcg package. Default is 0.5.

tolerance

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

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.

volume

Use input_volume instead.

Value

A ggseg_atlas object of type "cerebellar" with both sf geometry and 3D meshes.

Examples

if (FALSE) { # \dontrun{
atlas <- create_cerebellar_from_volume(
  input_volume = "cerebellar_parcellation.nii.gz"
)
} # }