In LCBC-UiO/ggsegExtra: Extra Utilities for the 'ggseg' and 'ggseg3d' Plotting Tools

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

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 r nrow(atlases) available atlases across r length(unique(atlases$Package)) packages. The packages, their repository name and location can be found with:

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. 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.

LCBC-UiO/ggsegExtra documentation built on May 9, 2022, 1:07 a.m.