Package: ggseg.formats 0.0.4.9011

ggseg.formats: Brain Atlas Data Structures for the 'ggsegverse' Ecosystem

Provides the 'ggseg_atlas' S3 class used across the 'ggsegverse' ecosystem for 2D and 3D brain visualisation. Ships four bundled atlases ('Desikan-Killiany', 'FreeSurfer' 'aseg', 'TRACULA', 'SUIT') and functions for querying, subsetting, renaming, and enriching atlas objects. Also includes readers for 'FreeSurfer' statistics files.

Authors:Athanasia Mo Mowinckel [aut, cre], Center for Lifespan Changes in Brain and Cognition, University of Oslo [cph]

ggseg.formats_0.0.4.9011.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggseg.formats/json (API)

# Install 'ggseg.formats' in R:
install.packages('ggseg.formats', repos = c('https://drmowinckels.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ggsegverse/ggseg.formats/issues

Pkgdown/docs site:https://ggsegverse.github.io

On CRAN:

Conda:

9.19 score 22 packages 89 scripts 1.1k downloads 9 mentions 74 exports 6 dependencies

Last updated from:36c8ad9071. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK182
source / vignettesOK175
linux-releaseOK170
macos-releaseOK124
macos-oldrelOK163
windows-develOK159
windows-releaseOK161
windows-oldrelOK172
wasm-releaseOK120

Exports:as_brain_atlasas_ggseg_atlasas_polygon_atlasas_sf_atlasasegassert_ggseg_atlasatlas_centerlinesatlas_context_removeatlas_core_addatlas_displayatlas_geomatlas_geometry_typeatlas_hemiatlas_labelsatlas_meshesatlas_paletteatlas_plot_paletteatlas_polygonsatlas_region_contextualatlas_region_keepatlas_region_opatlas_region_removeatlas_region_renameatlas_regionsatlas_sfatlas_structure_reorderatlas_typeatlas_verticesatlas_view_gatheratlas_view_keepatlas_view_removeatlas_view_remove_regionatlas_view_remove_smallatlas_view_reorderatlas_view_selectatlas_viewsattach_sfcbrain_atlasbrain_data_corticalbrain_data_subcorticalbrain_data_tractbrain_labelsbrain_regionsbrain_viewsconvert_legacy_brain_atlasdkget_brain_meshget_cerebellar_meshggseg_atlasggseg_data_cerebellarggseg_data_corticalggseg_data_subcorticalggseg_data_tractis_atlas_polygonis_atlas_sfis_brain_atlasis_cerebellar_atlasis_cortical_atlasis_ggseg_atlasis_ggseg3d_atlasis_subcortical_atlasis_tract_atlaslegacy_region_mapmigrate_atlas_filesread_atlas_filesread_freesurfer_statsread_freesurfer_tablerelabel_atlasreorder_sfcset_atlas_paletteset_atlas_typesuittraculaunify_legacy_atlases

Dependencies:cligeometrieslifecycleRcpprlangsfheaders

Migrating atlases and code
Migrating code to the 0.1.0 region keys | Do not use display for this | The accessors return rows, not a set | Adding display to your own atlas | label must be unique | 2D coverage is not validated | Migrating an atlas package to sf-optional | The recipe | What migrate_atlas_files() does | Keeping sf instead | Verifying the result

Last update: 2026-10-12
Started: 2026-06-11

The ggseg_atlas object
What is a ggseg_atlas? | Anatomy of an atlas | Three atlas types | Core: the region table | Querying an atlas | Extracting render-ready data | Checking and converting

Last update: 2026-10-12
Started: 2026-02-09

Customising brain atlases
The manipulation toolkit | Keeping and removing regions | Context regions | Renaming regions | Managing views | Cleaning up geometry | Reordering and gathering | Adding metadata | A full pipeline

Last update: 2026-10-12
Started: 2026-02-09

Readme and manuals

Help Manual

Help pageTopics
Coerce to ggseg atlasas_brain_atlas as_ggseg_atlas
Convert a ggseg atlas to the sf-optional polygon representationas_polygon_atlas
Rehydrate a ggseg atlas into sf-backed formas_sf_atlas
FreeSurfer Automatic Subcortical Segmentation Atlasaseg
Require a valid ggseg atlas, reporting why it is notassert_ggseg_atlas
Get atlas tract centerlinesatlas_centerlines
Extract the display-name column of an atlasatlas_display
Get the raw 2D geometry of an atlasatlas_geom
Classify or test an atlas's 2D geometryatlas_geometry_type is_atlas_polygon is_atlas_sf
Extract the hemisphere column of an atlasatlas_hemi
Extract the label column of an atlasatlas_labels brain_labels
Manipulate brain atlas regions and viewsatlas_context_remove atlas_core_add atlas_manipulation atlas_region_contextual atlas_region_keep atlas_region_op atlas_region_remove atlas_region_rename atlas_view_gather atlas_view_keep atlas_view_remove atlas_view_remove_region atlas_view_remove_small atlas_view_reorder atlas_view_select
Get atlas meshes for 3D renderingatlas_meshes
Get the palette of an atlasatlas_palette
Get a plottable palette for an atlasatlas_plot_palette
Get atlas polygons for 2D renderingatlas_polygons
Extract the region column of an atlasatlas_regions brain_regions
Get atlas data for 2D renderingatlas_sf
Reorder the structures of an atlasatlas_structure_reorder
Detect atlas typeatlas_type
Get atlas vertices for 3D renderingatlas_vertices
Get available views in atlasatlas_views brain_views
Attach an 'sfc' column and class a data frame as 'sf', without sfattach_sfc
Convert legacy ggseg atlases to ggseg_atlas formatconvert_legacy_brain_atlas unify_legacy_atlases
Desikan-Killiany Cortical Atlasdk
Get brain surface meshget_brain_mesh
Get SUIT cerebellar surface meshget_cerebellar_mesh
Constructor for ggseg atlasbrain_atlas ggseg_atlas
Create cerebellar atlas dataggseg_data_cerebellar
Create cortical atlas databrain_data_cortical ggseg_data_cortical
Create subcortical atlas databrain_data_subcortical ggseg_data_subcortical
Create tract atlas databrain_data_tract ggseg_data_tract
Check ggseg atlas classis_brain_atlas is_cerebellar_atlas is_cortical_atlas is_ggseg_atlas is_subcortical_atlas is_tract_atlas
Check if object is a legacy ggseg3d atlasis_ggseg3d_atlas
Map pre-0.1.0 region names to current region keyslegacy_region_map
Migrate atlas '.rda' files to the sf-optional polygon formatmigrate_atlas_files
Read in atlas data from all subjectsread_atlas_files
Read in raw FreeSurfer stats fileread_freesurfer_stats
Read in stats table from FreeSurferread_freesurfer_table
Re-key an atlas's labelsrelabel_atlas
Reorder an 'sfc' without sfreorder_sfc
Set the palette of an atlasset_atlas_palette
Set the type of an atlasset_atlas_type
SUIT Cerebellar Lobular Atlassuit
TRACULA White Matter Tract Atlastracula