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Description

Tri-Surface Mesh Plots for Brain Atlases.

Mainly contains a plotting function ggseg3d(), and data of two standard brain atlases (Desikan-Killiany and aseg). By far, the largest bit of the package is the data for each of the atlases. The functions and data enable users to plot tri-surface mesh plots of brain atlases, and customise these by projecting colours onto the brain segments based on values in their own data sets. Functions are wrappers for 'plotly'. Mowinckel & Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.

ggseg3d

Coveragestatus CRANstatus Lifecycle:maturing R buildstatus

This package mainly contains a plotting function ggseg3d and data.frames of different brain atlases for plotting. Plotting results of analyses on regions or networks often involves swapping between statistical tools, like R and Matlab, and software for brain imaging to correctly visualise analysis results.

This package aims to make it possible to plot results directly through R.

Atlases

There are currently four atlases available in the package:

  1. dk_3d - Desikan-Killiany atlas (aparc).
  2. aseg_3d - Automatic sub-cortical segmentation.

If you want to create your own custom atlas or discover other compatible atlases, please see the companion package ggsegExtra.

Installation

We recommend installing {ggsegExtra} through the ggseg r-universe.

# Enable this universe
options(repos = c(
    ggseg = 'https://ggseg.r-universe.dev',
    CRAN = 'https://cloud.r-project.org'))

# Install some packages
install.packages('ggsegExtra')

The package can be installed using {remotes}. The package includes some large datasets for the brain coordinates. Please be patient during download and install, it will take some time.

install.packages("remotes")
remotes::install_github("ggseg/ggseg3d", build_vignettes = TRUE)

The functions are now installed, and you may load them when you want to use them. All functions are documented in standard R fashion.

Use

The package also has a vignette, to help you get started using it. You can access it here, or via R:

library(ggseg3d)
vignette("ggseg3d")
p <- ggseg3d(atlas=dk_3d) %>% 
  remove_axes() %>% 
  pan_camera("right lateral")

p <- ggseg3d(atlas=aseg_3d) %>% 
  add_glassbrain() %>% 
  remove_axes() %>% 
  pan_camera("right lateral")

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 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.

Metadata

Version

1.6.3

License

Unknown

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