diff --git a/README.md b/README.md index 7f4027f2..9cc31400 100644 --- a/README.md +++ b/README.md @@ -2,11 +2,10 @@ [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/threeBrain)](https://cran.r-project.org/package=threeBrain) -[![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html) [![R-CMD-check](https://github.com/dipterix/threeBrain/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dipterix/threeBrain/actions/workflows/R-CMD-check.yaml) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![DOI](https://raw.githubusercontent.com/dipterix/threeBrain/master/inst/doi.svg)](https://doi.org/10.1016/j.neuroimage.2020.117341) - +[![DOI-RAVE](https://raw.githubusercontent.com/dipterix/threeBrain/master/inst/doi.svg)](https://doi.org/10.1016/j.neuroimage.2020.117341) +[![DOI-YAEL](https://img.shields.io/badge/DOI-10.1523%2FENEURO.0328--23.2023-blue?link=https%3A%2F%2Fdoi.org%2F10.1523%2FENEURO.0328-23.2023)](https://doi.org/10.1523/ENEURO.0328-23.2023) @@ -42,7 +41,7 @@ 1. [`R`](https://cran.r-project.org/) and [`RStudio Desktop (Free Version)`](https://posit.co/download/rstudio-desktop/) 2. Open `RStudio`, enter from its console: ```r -install.packages("threeBrain") +install.packages("threeBrain", repos = "https://rave-ieeg.r-universe.dev") ``` If you want to install `dev` version from *Github*, then use: ```r @@ -82,7 +81,7 @@ x <- freesurfer_brain2( fs_subject_folder = n27_path, ``` 2. Visualize ```r -plot(x) # alternatively, you can use `n27$plot()` +plot(x) # alternatively, you can use x$plot()` ``` ## C. Subject Setup @@ -145,33 +144,43 @@ The viewer will be in `N27` template, and electrodes of these two subjects can b ## F. Electrode Localization (`YAEL`) -`YAEL`: "Yet Another Electrode Localizer" is a module that has been integrated into [RAVE (R Analysis and Visualization of iEEG)](https://openwetware.org/wiki/RAVE). The paper will come out soon. Please contact RAVE team on how to localize electrodes. +[YAEL ("Your Advanced Electrode Localizer)](https://doi.org/10.1523/ENEURO.0328-23.2023) has been integrated into [RAVE (R Analysis and Visualization of iEEG)](https://openwetware.org/wiki/RAVE). Please check our website https://yael.wiki [Here is a `sfN` poster](https://www.dropbox.com/s/st0cw1aro4kmo2e/2022-poster-sfN-Zhengjia-RAVE_poster-07Nov22.pdf?dl=0) ## Citation -To cite threeBrain in publications use: +To cite `threeBrain` in publications use: -> Magnotti, J. F., Wang, Z., & Beauchamp, M. S. (2020). RAVE: Comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data. *NeuroImage, 223*, 117341. +* Wang, Z., Magnotti, J. F., Zhang, X., & Beauchamp, M. S. (2023). YAEL: Your Advanced Electrode Localizer. Eneuro, 10(10). +* Magnotti, J. F., Wang, Z., & Beauchamp, M. S. (2020). RAVE: Comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data. NeuroImage, 223, 117341. A BibTeX entry for LaTeX users: ``` - @Article{, - title = {{RAVE}: Comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data}, - author = {John F. Magnotti and Zhengjia Wang and Michael S. Beauchamp}, - journal = {NeuroImage}, - year = {2020}, - volume = {223}, - doi = {10.1016/j.neuroimage.2020.117341}, - pages = {117341}, - } +@Article{, + title = {{YAEL}: Your Advanced Electrode Localizer}, + author = {Zhengjia Wang and John F. Magnotti and Xiang Zhang and Michael S. Beauchamp}, + journal = {Eneuro}, + year = {2023}, + volume = {10}, + number = {10}, + publisher = {Society for Neuroscience}, + doi = {10.1523/ENEURO.0328-23.2023}, +} +@Article{, + title = {{RAVE}: Comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data}, + author = {John F. Magnotti and Zhengjia Wang and Michael S. Beauchamp}, + journal = {NeuroImage}, + year = {2020}, + volume = {223}, + doi = {10.1016/j.neuroimage.2020.117341}, + pages = {117341}, +} ``` ## License -This package as a whole is licensed under GPL-3.0. The front-end viewer does not contain GNU components. +The front-end viewer (JavaScript) and its components are licensed under MPL-2.0 free open-source license. This package (including the R code and viewer) as a whole is licensed under free open-source GPL-3.0. Please check `LICENSE` file for details. -Explanation: The viewer is considered "data" and might not be abide by GPL-3.0 license. However, certain software scripts are linked by the viewers. These software scripts use quite permissive license. Please check `LICENSE` file for details.