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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%",
echo = TRUE
)
library(ggsegExtra)
atlases <- ggseg_atlas_repos()
atlases <- atlases[grep("ggseg$|ggsegExtra$|ggseg3d$", atlases$Package, invert = TRUE),]
```
# ggsegExtra <img src="man/figures/logo.png" align="right" alt="" width="120" />
<!-- badges: start -->
[](https://codecov.io/gh/ggseg/ggsegExtra)
[](https://CRAN.R-project.org/package=ggsegExtra)
[](https://www.tidyverse.org/lifecycle/#stable)
[](https://github.com/ggseg/ggsegExtra/actions)
<!-- badges: end -->
This package contains information on verified atlases compatible for use in [ggseg](https://ggseg.github.io/ggseg) and [ggseg3d](https://ggseg.github.io/ggseg3d) plotting packages in R.
It also contains functions and pipelines to create custom atlases.
## Installing
We recommend installing this package from its [r-universe](https://ggseg.r-universe.dev/ui#builds) build:
```{r, eval = FALSE}
# Enable this universe
options(repos = c(
ggseg = 'https://ggseg.r-universe.dev',
CRAN = 'https://cloud.r-project.org'))
# Install some packages
install.packages('ggsegExtra')
```
Alternatively, install the package with the remotes package from github.
```{r, eval = FALSE}
# install.packages("remotes")
remotes::install_github("ggseg/ggsegExtra")
```
## Create custom atlases
We have tutorials on how to make atlases available in the `Articles` of the [package documentation page](https://ggseg.github.io/ggsegExtra/).
Currently, the pipeline for making 3d atlases needs FreeSufer to be installed on your system and a ready `.annot` file to use for the conversions.
Improvements to the pipeline in creating cortical atlases both for ggseg and ggseg3d is still being developed.
Pipelines for creating sub-cortical atlases of any kind are still in their infancy, and we do not yet have good solutions for their creation.
Suggestions for improvement are welcome through GH issues or direct Pull requests.
## Availale atlases
There are currently `r nrow(atlases)` available atlases across `r length(unique(atlases$Package))` packages.
The packages, their repository name and location can be found with:
```{r, echo = FALSE, results='asis'}
for (i in 1:nrow(atlases)) {
atl <- as.character(atlases[i, "Package"])
# find doi
readmeurl <- sprintf("https://raw.githubusercontent.com/ggseg/%s/main/README.Rmd", atl)
if(httr::http_error(readmeurl))
readmeurl <- sprintf("https://raw.githubusercontent.com/ggseg/%s/master/README.Rmd", atl)
readme <- readLines(readmeurl)
idx <- grep("badges: ", readme)
badges <- readme[(idx[1]+1):(idx[2]-1)]
badges <- c("", badges[c(grep("\\[!\\[R", badges), grep("\\[!\\[DOI", badges))])
cat(
sprintf('### [%s](%s)',
atl, atlases[i, "RemoteUrl"]),
sprintf('<img src="%s/raw/HEAD/man/figures/logo.png" align="right" alt="%s logo" width="120"/>',
atlases[i, "RemoteUrl"], atl),
badges,
sprintf("\n%s\n%s\n", atlases[i, "Title"], atlases[i, "Description"]),
sep = "\n"
)
}
```
## Code of Conduct
Please note that the ggsegExtra project is released with a [Contributor Code of Conduct](https://www.contributor-covenant.org/version/1/0/0/code-of-conduct.html). 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](https://github.com/ggseg/ggsegExtra/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.