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FIX: add more system deps for more recent ubuntu versions
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dfsp-spirit committed Nov 27, 2024
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# 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.

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* 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
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* [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: `?<function>`, where you replace `<function>` with a function name. Like this: `?group.morph.native`.
* Run `example(<function>)` to see a live demo that uses the function `<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.
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