README.md

In neuroconductor-devel-releases/ggsegExtra: Plotting tool for brain atlases

ggsegExtra

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

Atlases

There are currently three atlases available in the package:

2d polygon atlases

1. midsagittal - mid-sagittal slice showing the cerebellum, 3rd and 4th ventricles, corpus callosum etc.
2. glasser - HCP cortical segmentation (Glasser et al. 2015)
3. jhu- Hua et al. 2008, JHU white-matter tractography atlas
4. yeo7- Yeo et al. 7 resting state networks
5. yeo17- Yeo et al. 17 resting state networks
6. tracula - Yendiki et al. probabilistic white matter tractopraphy

3d mesh atlases

1. glasser_3d - HCP cortical segmentation (Glasser et al. 2015)
2. desterieux_3d - Desterieux et al. cortical segmentation
3. yeo7_3d - Yeo et al. 7 resting state networks
4. yeo17_3d- Yeo et al. 17 resting state networks
5. schaefer7- Schaefer et al. 7 resting state networks
6. schaefer17- Schaefer et al. 17 resting state networks
7. tracula_3d - Yendiki et al. probabilistic white matter tractopraphy
8. jhu_3d- Hua et al. 2008, JHU white-matter tractography atlas
9. icbm_3d- JHU labels from Mori et al. (2005)

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 it 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!

Use

You will need to use the ggseg package to use these atlases, or wrangle them your self. You can access it here, or via R:

devtools::install_github("LCBC-UiO/ggseg")

Make sure to always load the ggsegExtra package after the ggseg package.

library(ggseg)
library(ggsegExtra)

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

neuroconductor-devel-releases/ggsegExtra documentation built on Oct. 22, 2020, 4:47 p.m.