Plotting tool for brain atlases
Athanasia Mowinckel & Didac Vidal Pineiro
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
This package aims to make it possible to plot results directly through R.
There are currently three atlases available in the package:
dkt- Desikan-Killany atlas (aparc).
yeo7- Yeo 2011 7 resting-state networks.
yeo17- Yeo 2011 17 resting-state network.
aseg- Automatic subcortical segmentation.
midsagittal- mid-sagittal slice showing the cerebellum, 3rd and 4th ventricles, corpus callosum etc.
glasser- HCP cortical segmentation (Glasser et al. 2015)
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
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!
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.
The package also has a vignette, to help you get started using it. You can access it here, or via R:
You can also see one of the creators blog for introductions to its use here