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Create cerebellar atlas from SUIT flatmap

Source: R/atlas_cerebellar.R
create_cerebellar_from_gifti.Rd

[Experimental]

Turn SUIT cerebellar parcellation files into a brain atlas you can plot with ggseg and ggseg3d. Reads GIFTI label files containing vertex-to-region assignments and projects them onto the SUIT flatmap surface to generate 2D polygon geometry. Optionally tessellates per-region 3D meshes from a cerebellar segmentation volume.

The SUIT (Spatially Unbiased Infratentorial Template) flatmap is a standard 2D representation of the cerebellar cortex. Unlike cortical atlases that require orthographic projection of an inflated mesh, the flatmap surface already contains 2D coordinates.

Usage

create_cerebellar_from_gifti(
  gifti_files,
  volume = NULL,
  atlas_name = NULL,
  output_dir = NULL,
  decimate = 0.5,
  tolerance = NULL,
  smooth_refinements = NULL,
  cleanup = NULL,
  verbose = get_verbose(),
  skip_existing = NULL
)

Arguments

gifti_files

Character vector of paths to GIFTI label files (.label.gii or .func.gii) containing the cerebellar parcellation.

volume

Optional path to a cerebellar segmentation volume (NIfTI) for 3D mesh generation. When provided, per-region meshes are tessellated using FreeSurfer tools and included in the atlas for 3D rendering.

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

[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 of type "cerebellar" containing region metadata (core), a colour palette, sf geometry for 2D plots, and optionally 3D meshes.

Examples

if (FALSE) { # \dontrun{
atlas <- create_cerebellar_from_gifti(
  gifti_files = "Lobules-SUIT.label.gii"
)
ggseg(atlas = atlas)
} # }