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Plotting tool for brain atlases

Athanasia Mowinckel & Didac Vidal Pineiro

Travis build status AppVeyor build status

Coverage status

This package mainly contains a plotting function ggseg 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 three atlases available in the package:

  1. dkt - Desikan-Killany atlas (aparc).
  2. yeo7 - Yeo 2011 7 resting-state networks.
  3. yeo17 - Yeo 2011 17 resting-state network.
  4. aseg - Automatic subcortical segmentation.
  5. midsagittal - mid-sagittal slice showing the cerebellum, 3rd and 4th ventricles, corpus callosum etc.
  6. glasser - HCP cortical segmentation (Glasser et al. 2015)
  7. jhu- JHU white-matter tractography atlas

We are working on creating a detailed description in the wiki on how to create and contribute atlases to the package. The ggseg function already allows you to provide it with a data.frame of a custom atlas if you have it, but is must correspond to certain specifications to work.

Please see the wiki for information on adding atlases, or inspect the included datasets for requirements. If anything is unclear in the wiki, give us a shout out in the issues!

Installation

The package can be installed using devtools:

install.packages("devtools")
devtools::install_github("LCBC-UiO/ggseg", 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(ggseg)
vignette("ggseg")

You can also see one of the creators blog for introductions to its use here

Included atlases and palettes