Package: ggseg.formats 0.0.4

Athanasia Mo Mowinckel

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.tar.gz
ggseg.formats_0.0.4.tar.gz(r-4.7-any)ggseg.formats_0.0.4.tar.gz(r-4.6-any)
ggseg.formats_0.0.4.tgz(r-4.6-emscripten)
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://cran.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:

7.47 score 21 packages 68 scripts 1.3k downloads 9 mentions 61 exports 6 dependencies

Last updated from:e80a98012e. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK173
source / vignettesOK234
linux-release-x86_64OK175
wasm-releaseOK165

Exports:as_brain_atlasas_ggseg_atlasas_polygon_atlasas_sf_atlasasegatlas_context_removeatlas_core_addatlas_geomatlas_geometry_typeatlas_labelsatlas_meshesatlas_paletteatlas_polygonsatlas_region_contextualatlas_region_keepatlas_region_opatlas_region_removeatlas_region_renameatlas_regionsatlas_sfatlas_typeatlas_verticesatlas_view_gatheratlas_view_keepatlas_view_removeatlas_view_remove_regionatlas_view_remove_smallatlas_view_reorderatlas_viewsbrain_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_atlasmigrate_atlas_filesread_atlas_filesread_freesurfer_statsread_freesurfer_tablesuittraculaunify_legacy_atlases

Dependencies:cligeometrieslifecycleRcpprlangsfheaders

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
Rendered fromatlas-manipulation.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2026-02-18

Migrating atlas packages to sf-optional
The recipe | What migrate_atlas_files() does | Keeping sf instead | Verifying the result
Rendered frommigrating-atlases.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2026-06-18

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
Rendered fromggseg.formats.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2026-02-18

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
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 unique labels from 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
Get atlas meshes for 3D renderingatlas_meshes
Get atlas paletteatlas_palette
Get atlas polygons for 2D renderingatlas_polygons
Extract unique region names from an atlasatlas_regions brain_regions
Get atlas data for 2D renderingatlas_sf
Detect atlas typeatlas_type
Get atlas vertices for 3D renderingatlas_vertices
Get available views in atlasatlas_views brain_views
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
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
SUIT Cerebellar Lobular Atlassuit
TRACULA White Matter Tract Atlastracula