diff --git a/README.md b/README.md index 0c9e9ac..dedd9ae 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # fsbrain -[![DOI](https://zenodo.org/badge/209085379.svg)](https://zenodo.org/doi/10.5281/zenodo.3559816) +[![DOI](https://zenodo.org/badge/209085379.svg)](https://zenodo.org/doi/10.5281/zenodo.3559816) An R package for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data (e.g. cortical thickness) for individual subjects and groups. @@ -67,8 +67,12 @@ R packages are compiled from source by default under Linux, so you need some dev * for deb-based Linux distributions (Debian, Ubuntu, ...): ```shell -sudo apt-get install libmagick++-dev libx11-dev libgl1-mesa-dev libglu1-mesa-dev mesa-common-dev libfreetype6-dev libxml2-dev libssh-dev libcurl4-openssl-dev libgfortran4 +sudo apt-get install libmagick++-dev libx11-dev libgl1-mesa-dev libglu1-mesa-dev mesa-common-dev libfreetype6-dev libxml2-dev libssh-dev libcurl4-openssl-dev gfortran libblas-dev liblapack-dev libgfortran4 ``` + +Note: For recent Ubuntu versions, you may have to replace ```libgfortan4``` in the command above with ```libgfortan5```. + + * for rpm-based Linux distributions (Fedora, CentOS, RHEL, ...): ```shell sudo yum install ImageMagick-c++-devel libX11-devel mesa-libGLU-devel freetype-devel libxml2-devel @@ -99,14 +103,14 @@ The documentation can be accessed from within an R session after you have loaded * [basic fsbrain example notebook](https://htmlpreview.github.io/?https://github.com/dfsp-spirit/fsbrain/blob/develop/web/Rmd_web_examples/examples.html): Live visualization of subject data * [advanced fsbrain example notebook](https://htmlpreview.github.io/?https://github.com/dfsp-spirit/fsbrain/blob/develop/web/Rmd_web_examples/examples_adv.html): Plotting group data * [export API fsbrain example notebook](https://htmlpreview.github.io/?https://github.com/dfsp-spirit/fsbrain/blob/develop/web/Rmd_web_examples/examples_export.html): Exporting publication-ready plots - - + + * Detailed vignettes with explanations and examples for the functions of the package is included, run `browseVignettes("fsbrain")` to see the vignettes. You can also open the vignette directly: * How to load and visualize surface-based neuroimaging data: `vignette("fsbrain")` or: [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain.html) * How to load and visualize volume-based neuroimaging data: `vignette("fsbrain_vol")` or: [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain_vol.html) * The fsbrain FAQ: `vignette("fsbrain_faq")` or: [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain_faq.html) - - + + * Help for a specific function can be accessed in the usual R manner: `?`, where you replace `` with a function name. Like this: `?group.morph.native`. * Run `example()` to see a live demo that uses the function ``. Like this: `example(group.morph.native)`. * The [unit tests](./tests/testthat/) that come with this package are essentially a list of examples that illustrate how to use the functions.