ggseg.formats

ggseg.formats 0.0.2

Deep cerebellar nuclei support

• ggseg_data_cerebellar() gains an optional meshes parameter for deep cerebellar structures (e.g. dentate, interposed, fastigial nuclei) that are not on the SUIT cortical surface. Surface regions use vertices (shared SUIT mesh), deep structures use individual meshes (like subcortical atlases).
• Validation now checks the union of vertices + meshes labels against core when both are present, rather than requiring each to cover all labels independently.
• rebuild_atlas_data() preserves cerebellar data type and handles mixed vertices + meshes correctly.

Bug fixes

• reposition_views() now handles sfc_GEOMETRY (mixed geometry types) by casting to MULTIPOLYGON before coordinate operations.
• atlas_view_gather() is more robust against non-sf or empty sf data, preventing errors in subcortical and tract pipelines.

ggseg.formats 0.0.1

Initial CRAN release. Extracts and formalises the atlas data structures that were previously embedded in ggseg and ggseg3d.

Unified ggseg_atlas S3 class

• ggseg_atlas() constructor with typed data containers for cortical, subcortical, tract, and cerebellar atlases.
• Type-checking predicates: is_ggseg_atlas(), is_cortical_atlas(), is_subcortical_atlas(), is_tract_atlas(), is_cerebellar_atlas().
• Coercion with as_ggseg_atlas(), as.data.frame(), and as.list() methods.
• plot() method for quick atlas visualisation via ggplot2.

Accessors

• atlas_type(), atlas_regions(), atlas_labels(), atlas_palette(), atlas_sf(), atlas_vertices(), atlas_meshes(), and atlas_views() for querying atlas contents without reaching into slots.

Atlas manipulation

• Pipe-friendly region operations: atlas_region_keep(), atlas_region_remove(), atlas_region_rename(), atlas_region_contextual().
• Metadata enrichment with atlas_core_add().
• View management: atlas_view_keep(), atlas_view_remove(), atlas_view_remove_region(), atlas_view_remove_small(), atlas_view_gather(), atlas_view_reorder().

Bundled atlases

• Ships three ready-to-use atlases: dk() (Desikan-Killiany cortical), aseg() (FreeSurfer subcortical), and tracula() (white matter tracts).
• get_brain_mesh() and get_cerebellar_mesh() provide 3D surface meshes for rendering.

Legacy conversion

• convert_legacy_brain_atlas() and unify_legacy_atlases() bridge old ggseg/ggseg3d atlas objects to the unified format.
• Deprecated wrappers (brain_atlas(), brain_regions(), etc.) ease migration from the old API.

FreeSurfer I/O

• read_freesurfer_stats(), read_atlas_files(), and read_freesurfer_table() for reading FreeSurfer statistics into R.