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ggseg3d

Coverage Status CRAN status downloads Lifecycle: stable code-quality R-CMD-check

Interactive 3D brain atlas visualization in R. Plot brain parcellations as WebGL meshes powered by Three.js, or render publication-quality static images through rgl and rayshader. A pipe-friendly API lets you map data onto brain regions, control camera angles, toggle region edges, overlay glass brains, and snapshot the result.

Installation

Install from CRAN:

install.packages("ggseg3d")

Or get the development version from the ggsegverse r-universe:

options(
  repos = c(
    ggsegverse = "https://ggsegverse.r-universe.dev",
    CRAN = "https://cloud.r-project.org"
  )
)
install.packages("ggseg3d")

Atlases

Three atlases ship with the package (via ggseg.formats):

  1. dk – Desikan-Killiany cortical atlas
  2. aseg – Automatic subcortical segmentation
  3. tracula – White-matter tract atlas

Additional atlases are available through the ggsegverse r-universe.

Usage

ggseg3d(atlas = dk(), hemisphere = "left") |>
  pan_camera("left lateral")

Subcortical structures with a translucent glass brain overlay:

ggseg3d(atlas = aseg()) |>
  add_glassbrain() |>
  pan_camera("right lateral")

See the package website for the full walkthrough, rayshader rendering, and Shiny integration.

Citation

Mowinckel & Vidal-Piñeiro (2020). Visualization of Brain Statistics With R Packages ggseg and ggseg3d. Advances in Methods and Practices in Psychological Science. doi:10.1177/2515245920928009

Funding

This tool is partly funded by:

EU Horizon 2020 Grant: Healthy minds 0-100 years: Optimising the use of European brain imaging cohorts (Lifebrain).

Grant agreement number: 732592.

Call: Societal challenges: Health, demographic change and well-being

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.