Plotting Tool for Brain Atlases

Provides a 'ggplot2' geom and position for visualizing brain region data on cortical, subcortical, and white matter tract atlases. Brain atlas geometries are stored as polygon data, enabling seamless integration with the 'ggplot2' ecosystem including faceting, custom scales, and themes. Mowinckel & Vidal-Piñeiro (2020) .

ggseg

Neuroimaging analyses produce region-level results – cortical thickness, p-values, network assignments – that need to end up on a brain figure. ggseg stores brain atlas geometries as simple features and plots them as ggplot2 layers, so you get publication-ready brain figures with the same code you’d use for any other ggplot.

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

Installation

Install from CRAN:

install.packages("ggseg")

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("ggseg")

Quick start

library(ggseg)
library(ggplot2)

Built-in atlases

ggseg ships with three atlases: dk (Desikan-Killiany cortical parcellation), aseg (automatic subcortical segmentation), and tracula (white matter tracts). plot() gives you a quick overview:

plot(dk())
plot(aseg())

Figure 1: Overview of the dk and aseg built-in brain atlases.

Figure 2: Overview of the dk and aseg built-in brain atlases.

Plotting your own data

Pass a data frame to ggplot() with a column that matches the atlas (typically region or label). geom_brain() handles the join:

library(dplyr)

some_data <- tibble(
  region = rep(
    c(
      "transverse temporal",
      "insula",
      "precentral",
      "superior parietal"
    ),
    2
  ),
  p = sample(seq(0, .5, .001), 8),
  groups = c(rep("g1", 4), rep("g2", 4))
)

ggplot(some_data) +
  geom_brain(
    atlas = dk(),
    position = position_brain(hemi ~ view),
    aes(fill = p)
  ) +
  facet_wrap(~groups) +
  scale_fill_viridis_c(option = "cividis", direction = -1) +
  theme_void()

More atlases

Many additional atlases are available through the ggsegverse r-universe:

install.packages("ggsegYeo2011", repos = "https://ggsegverse.r-universe.dev")

Learn more

The package website has vignettes covering external data, view positioning, the geom_sf() workflow, and reading FreeSurfer stats files.

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.