This package contains information on verified atlases compatible for use in ggseg and ggseg3d plotting packages in R. It also contains functions and pipelines to create custom atlases.

## Installing

We recommend installing this package from its r-universe build:

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

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

Alternatively, install the package with the remotes package from github.

# install.packages("remotes")
remotes::install_github("ggseg/ggsegExtra")

## Create custom atlases

We have tutorials on how to make atlases available in the Articles of the package documentation page. Currently, the pipeline for making 3d atlases needs FreeSufer to be installed on your system and a ready .annot file to use for the conversions. Improvements to the pipeline in creating cortical atlases both for ggseg and ggseg3d is still being developed. Pipelines for creating sub-cortical atlases of any kind are still in their infancy, and we do not yet have good solutions for their creation. Suggestions for improvement are welcome through GH issues or direct Pull requests.

## Availale atlases

There are currently 23 available atlases across 23 packages. The packages, their repository name and location can be found with:

### ggsegEconomo

economo datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the economo atlases to plot using functions from those two packages.

### ggsegFlechsig

Flechsig datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Flechsig atlases to plot using functions from those two packages.

### ggsegKleist

Kleist datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the historical Kleist atlases to plot using functions from those two packages.

### ggsegBrodmann

brodmann datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the brodmann area atlases to plot using functions from those two packages.

### ggsegCampbell

Campbell(1905) datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Campbell

(1905) atlases to plot using functions from those two packages.

### ggsegIca

ica datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the ica atlases to plot using functions from those two packages.

### ggsegArslan

arslan datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the arslan atlases to plot using functions from those two packages.

### ggsegGordon

gordon datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the gordon atlases to plot using functions from those two packages.

### ggsegAicha

aicha datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the aicha atlases to plot using functions from those two packages.

### ggsegAal

aal datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the aal atlases to plot using functions from those two packages.

### ggsegPower

power datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the power atlases to plot using functions from those two packages.

### ggsegBrainnetome

Brainnetome datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Brainnetome atlases to plot using functions from those two packages.

### ggsegJHU

JHU datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the JHU atlases to plot using functions from those two packages.

### ggsegHO

Harvard-Oxford datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Harvard-Oxford cortical atlases to plot using functions from those two packages.

### ggsegICBM

ICBM datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the ICBM atlases to plot using functions from those two packages.

### ggsegDefaultExtra

Extra dk and aseg datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the extra dk and aseg, with some minor differences from the original atlases to plot using functions from those two packages.

### ggsegDKT

Desikan-Killiany-Tourville datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the DKT atlases to plot using functions from those two packages.

### ggsegTracula

Tracula datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Tracula atlases to plot using functions from those two packages.

### ggsegChen

Chen datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Chen atlases to plot using functions from those two packages.

### ggsegDesterieux

Desterieux datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Desterieux atlases to plot using functions from those two packages.

### ggsegSchaefer

Schaefer datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Schaefer atlases to plot using functions from those two packages.

### ggsegGlasser

Glasser datasets for the ggseg-plotting tool This is a support package for the ggseg, and ggseg3d packages. It contains the Glasser atlases to plot using functions from those two packages.

### ggsegYeo2011

Yeo 2011 Datasets for the ‘ggseg’-Package This is a support package for the ggseg, and ggseg3d packages. It contains the Yeo 2011 atlases to plot using functions from those two packages.

## Code of Conduct

Please note that the ggsegExtra project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

### 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 work is funded by EU Horizon 2020 Grant ‘Healthy minds 0-100 years: Optimizing the use of European brain imaging cohorts (Lifebrain)’, with grant agreement 732592. The project has also received funding from the European Research Council’s Starting grant (grant agreements 283634, to Anders Martin Fjell and 313440 to Kristine Beate Walhovd) and Consolidator Grant (grant agreement 771355 to Kristine Beate Walhovd and 725025 to Anders Martin Fjell). The project has received funding through multiple grants from the Norwegian Research Council.