This package provides pipelines for creating brain atlas data sets compatible with the ggseg and ggseg3d plotting packages in R.

Installing

Install from CRAN:

install.packages("ggseg.extra")

Or install the development version from r-universe:

options(
  repos = c(
    ggsegverse = "https://ggsegverse.r-universe.dev",
    CRAN = "https://cloud.r-project.org"
  )
)
install.packages("ggseg.extra")

Or from GitHub:

# install.packages("remotes")
remotes::install_github("ggsegverse/ggseg.extra")

Development version of freesurfer

The atlas creation functions require a development version of the freesurfer R package that is not yet on CRAN. Until the PR is merged, install from:

pak::pak("drmowinckels/freesurfer@refactor")

Create custom atlases

Tutorials are available in the Articles of the package documentation page. The cortical pipeline projects inflated mesh triangles directly to 2D polygons — atlas creation takes seconds and needs only FreeSurfer to read annotation files (no rendering, ImageMagick, or Chrome). Subcortical and tract pipelines are also available. Suggestions for improvement are welcome through GH issues or direct Pull requests.

Code of Conduct

Please note that the ggseg.extra project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Report bugs or requests

Don’t hesitate to ask for support using github issues, or requesting new atlases. While we would love getting help in creating new atlases, you may also request atlases through the issues, and we will try to get to it.

Funding

This work is funded by EU Horizon 2020 Grant ‘Healthy minds 0-100 years: Optimizing the use of European brain imaging cohorts (Lifebrain)’, with grant agreement 732592. The project has also received funding from the European Research Council’s Starting grant (grant agreements 283634, to Anders Martin Fjell and 313440 to Kristine Beate Walhovd) and Consolidator Grant (grant agreement 771355 to Kristine Beate Walhovd and 725025 to Anders Martin Fjell). The project has received funding through multiple grants from the Norwegian Research Council.