ggsegExtra

This package contains extra atlases for the use in the ggseg plotting package in R.

Atlases

There are currently 19 available atlases across 10 packages. The packages, their repository name and location can be found with:

library(ggsegExtra)

# List all verified compatible atlases
ggseg_atlas_repos()
#> # A tibble: 10 x 5
#>    repo                ggseg ggseg3d source comment                             
#>    <chr>               <lgl> <lgl>   <chr>  <chr>                               
#>  1 LCBC-UiO/ggsegYeo2… TRUE  TRUE    github both 17 and 7 Network data          
#>  2 LCBC-UiO/ggsegDest… FALSE TRUE    github the 2009 atlas                      
#>  3 LCBC-UiO/ggsegChen  FALSE TRUE    github both thickness and area maps        
#>  4 LCBC-UiO/ggsegScha… FALSE TRUE    github both 17 and 7 networks              
#>  5 LCBC-UiO/ggsegGlas… TRUE  TRUE    github full atlas                          
#>  6 LCBC-UiO/ggsegJHU   TRUE  TRUE    github white tract atlas                   
#>  7 LCBC-UiO/ggsegTrac… TRUE  TRUE    github white tract atlas                   
#>  8 LCBC-UiO/ggsegICBM  FALSE TRUE    github white tract atlas                   
#>  9 LCBC-UiO/ggsegHO    TRUE  FALSE   github Harvard-Oxford cortical (FSL)       
#> 10 LCBC-UiO/ggsegDefa… TRUE  FALSE   github extra 2d view for dk, p/a division …

We have two tutorials on how to make atlases available in the package documentation page. Currently, the pipeline for making 3d atlases is complete given Freesufer is installed on your system and you have a ready .annot file to use for the converions. Creating 2d atlases is currently still a work in progress, and we are not able to provide a better solution than the one described at the moment. We hope to remedy this in the near future.

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 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