Package: ggseg.extra 1.9.9.9015

Athanasia Mo Mowinckel

ggseg.extra: Create Brain Atlases for the 'ggsegverse' Plotting Ecosystem

Create brain atlas data sets compatible with the 'ggsegverse' plotting packages. Provides pipelines for building cortical, subcortical, white-matter tract, and cerebellar atlases from 'FreeSurfer' annotation files, 'GIFTI' and 'CIFTI' surface formats, 'neuromaps', cerebellar flatmaps, and volumetric 'NIfTI' images.

Authors:Athanasia Mo Mowinckel [aut, cre], Didac Vidal-Piñeiro [ctb], John Muschelli [ctb], Center for Lifespan Changes in Brain and Cognition, University of Oslo [cph]

ggseg.extra_1.9.9.9015.tar.gz
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ggseg.extra_1.9.9.9015.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggseg.extra/json (API)

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

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

On CRAN:

Conda:

8.31 score 66 stars 71 scripts 9 mentions 54 exports 103 dependencies

Last updated from:df1740aeaf. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK390
source / vignettesOK287
linux-releaseOK400
macos-releaseOK192
macos-oldrelOK194
windows-develOK340
windows-releaseOK265
windows-oldrelOK246
wasm-releaseOK206

Exports:as_verbosityaseg_contextaseg_hidden_labelsaseg_subcortical_labelsatlas_github_actionsatlas_simplifyatlas_smoothconvert_legacy_brain_atlascoregister_volumecreate_cerebellar_from_annotationcreate_cerebellar_from_gifticreate_cerebellar_from_volumecreate_cortical_from_annotationcreate_cortical_from_cifticreate_cortical_from_gifticreate_cortical_from_labelscreate_cortical_from_neuromapscreate_subcortical_from_volumecreate_tract_from_tractographycreate_tract_from_volumecreate_wholebrain_from_volumeget_ctabget_lutget_verboseis_ctabis_lutis_verboselut_addlut_combinemri_surf2surf_reregnew_project_setup_atlas_repoprepare_subcortical_anatomicalprepare_subcortical_mni152project_volume_anatomicalread_annotation_dataread_cifti_annotationread_ctabread_gifti_annotationread_lutread_neuromaps_annotationread_neuromaps_volumeread_suit_parcellationread_tractographysetup_atlas_reposetup_sitrepsubcortical_slabssubcortical_viewssuit_3d_pathsuit_deformation_fieldsuit_flatmap_pathtransform_mni_to_suituse_atlas_github_actionswrite_ctabwrite_lut

Dependencies:AsioHeadersbase64encbitbit64bslibcachemcallrchromoteclassclassIntclicliprcodetoolscpp11crayoncurlDBIdigestdplyre1071evaluatefarverfastmapfontawesomefsfurrrfuturegenericsgeojsonsfgeometriesggplot2ggsegggseg.formatsggseg3dglobalsgluegtablehighrhmshtmltoolshtmlwidgetsisobandjquerylibjsonifyjsonliteKernSmoothknitrlabelinglaterlatticelifecyclelistenvmagrittrmemoisemimeotelparallellypillarpkgconfigprettyunitsprocessxprogressprogressrpromisesproxypspurrrR6rapidjsonrrappdirsRColorBrewerRcppreadrrlangrmapshaperrmarkdowns2S7sassscalessfsfheadersspstringistringrtibbletidyrtidyselecttinytextzdbunitsutf8V8vctrsviridisLitevroomwebshot2websocketwithrwkxfunyamlzip

Contributing an atlas package
Requirements | Setting up the package repository | Edit DESCRIPTION | Create your atlas | How atlas data is stored | Document your atlas | Getting tests to pass | Multiple atlases in one package | Getting package checks to pass | Adding your package to r-universe | 1. Fork the r-universe repository | 2. Edit packages.json | 3. Submit a pull request | 4. Wait for review | Installing from r-universe | Updating your package
Rendered fromcontributing.Rmdusingknitr::rmarkdown

Last update: 2026-07-22
Started: 2026-03-18

Pipeline configuration
Parameter hierarchy | Available options | Setting options in R | Verbosity | Cleanup | Skip existing | Geometry parameters | Environment variables | Overriding defaults | Recipes | Development and debugging | Production and CI | Iterating on simplification level
Rendered frompipeline-configuration.Rmdusingknitr::rmarkdown

Last update: 2026-07-22
Started: 2026-03-18

Post-processing atlases
Inspecting an atlas | Removing regions | Keeping regions | Context regions | Labels versus regions | Adding metadata columns | View management | Keeping specific views | Removing views | Reordering views | Removing small regions from views | Gathering views | Adjusting geometry after the fact | Smoothing rough contours | Keeping the brain outline crisp | Rebuilding the atlas | Putting it together
Rendered frompost-processing.Rmdusingknitr::rmarkdown

Last update: 2026-07-22
Started: 2026-03-18

System setup
What each pipeline needs | FreeSurfer | ImageMagick | Chrome / Chromium | Parallel processing | Progress bars | Checking your setup
Rendered fromsystem-setup.Rmdusingknitr::rmarkdown

Last update: 2026-07-22
Started: 2026-03-18

Getting started with ggseg.extra
What's inside a ggseg_atlas | Cortical pipeline | Subcortical and tract pipelines | Post-processing | System requirements | Tutorials
Rendered fromggseg.extra.Rmdusingknitr::rmarkdown

Last update: 2026-03-29
Started: 2026-03-18

Converting legacy atlases
The old system | The current system | Converting old atlases | From a ggseg3d_atlas only | From both 2D and 3D objects | From a 2D ggseg_atlas only | Specifying atlas type | Batch conversion | Post-conversion checklist | Lessons learned from batch conversion | 3D data is not always preserved | Palette entries may not match core rows exactly | Labels with special characters lose sf coverage | Skip ggseg3d tests for atlases without 3D data | Troubleshooting | When to recreate instead
Rendered fromlegacy-conversion.Rmdusingknitr::rmarkdown

Last update: 2026-03-18
Started: 2026-03-18

Readme and manuals

Help Manual

Help pageTopics
Coerce a value to a verbosity levelas_verbosity
Reduce a subcortical atlas to focus regions on grey anatomical contextaseg_context
Standard FreeSurfer aseg labels stripped from a subcortical atlasaseg_hidden_labels
Lumped aseg subcortical structures a parcellation typically subdividesaseg_subcortical_labels
Workflows 'use_atlas_github_actions()' can writeatlas_github_actions
Smooth and simplify atlas 2D contoursatlas_simplify atlas_smooth
Coregister an atlas volume to a FreeSurfer subjectcoregister_volume
Create cerebellar atlas from FreeSurfer annotationcreate_cerebellar_from_annotation
Create cerebellar atlas from SUIT flatmapcreate_cerebellar_from_gifti
Create cerebellar atlas from volume segmentationcreate_cerebellar_from_volume
Create cortical atlas from FreeSurfer annotationcreate_cortical_from_annotation
Create cortical atlas from a CIFTI filecreate_cortical_from_cifti
Create cortical atlas from GIFTI annotation filescreate_cortical_from_gifti
Create brain atlas from label filescreate_cortical_from_labels
Create cortical atlas from a neuromaps annotationcreate_cortical_from_neuromaps
Create brain atlas from subcortical segmentationcreate_subcortical_from_volume
Create brain atlas from white matter tractscreate_tract_from_tractography
Create a white matter tract atlas from a label volumecreate_tract_from_volume
Create atlas from whole-brain volumetric parcellationcreate_wholebrain_from_volume
Read LUT and add hex coloursget_ctab get_lut
Get verbose settingget_verbose
Check if object is a LUTis_ctab is_lut
Get verbosity levelis_verbose
Add rows to a FreeSurfer LUTlut_add
Combine FreeSurfer LUTslut_combine
Re-register an annotation filemri_surf2surf_rereg
Prepare an atlas for the subcortical pipeline with anatomical contextprepare_subcortical_anatomical
Embed MNI152 subcortical parcels in a FreeSurfer aseg for grey-brain contextprepare_subcortical_mni152
Project atlas labels onto FreeSurfer anatomical contextproject_volume_anatomical
Read annotation data from filesread_annotation_data
Read CIFTI annotation fileread_cifti_annotation
Read GIFTI annotation filesread_gifti_annotation
Read FreeSurfer LUTread_ctab read_lut
Read neuromaps annotation filesread_neuromaps_annotation
Read neuromaps volume annotation via surface projectionread_neuromaps_volume
Read SUIT cerebellar parcellation from GIFTIread_suit_parcellation
Read tractography fileread_tractography
Create a new ggseg atlas packagesetup_atlas_repo
Check ggseg.extra setup statussetup_sitrep
Build subcortical slabs from a label bounding boxsubcortical_slabs subcortical_views
Path to bundled SUIT 3D cerebellar surfacesuit_3d_path
Download SUIT deformation field for MNI-to-SUIT transformssuit_deformation_field
Path to bundled SUIT flatmap surfacesuit_flatmap_path
Transform a volume from MNI space to SUIT cerebellar spacetransform_mni_to_suit
Add ggsegverse GitHub Actions workflows to a packageuse_atlas_github_actions
Write FreeSurfer LUTwrite_ctab write_lut