ggseg.formats (version 0.0.1)

convert_legacy_brain_atlas: Convert legacy ggseg atlases to ggseg_atlas format

Description

Convert old-style ggseg (2D) and ggseg3d (3D) atlases into the new ggseg_atlas format. This is a bridge function for working with existing atlases during the transition period.

For new atlases, use ggsegExtra::create_cortical_atlas() or ggsegExtra::create_subcortical_atlas() instead - they produce better results with proper vertex indices.

The function handles three scenarios:

• Both 2D and 3D: Merges geometry with vertex data

• 3D only: Extracts vertices, infers indices from mesh coordinates

• 2D only: Keeps geometry, 3D rendering unavailable

If the 3D atlas already contains vertex indices (newer ggseg3d atlases), those are preserved. Otherwise, vertex indices are inferred from mesh coordinates using hash-based matching (no FreeSurfer needed).

Usage

convert_legacy_brain_atlas(
  atlas_2d = NULL,
  atlas_3d = NULL,
  atlas_name = NULL,
  type = NULL,
  surface = "inflated",
  brain_meshes = NULL
)
unify_legacy_atlases(
  atlas_2d = NULL,
  atlas_3d = NULL,
  atlas_name = NULL,
  type = NULL,
  surface = "inflated",
  brain_meshes = NULL
)

Value

A ggseg_atlas object.

Arguments

atlas_2d

A ggseg_atlas (or legacy brain_atlas) with 2D geometry, or NULL.

atlas_3d

A ggseg3d_atlas with mesh data, or NULL.

atlas_name

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

type

Atlas type: "cortical" or "subcortical". If NULL, inferred from the input atlases.

surface

Which surface to match against when inferring vertices (e.g., "inflated"). Must match the 3D atlas surface exactly.

brain_meshes

Optional user-supplied brain meshes for vertex inference.

Examples

# \donttest{
new_atlas <- convert_legacy_brain_atlas(atlas_2d = dk())
# }