These notebooks were developed to be presented at the TrainTrack 2021 edition of the OHBM BrainHack.
This short series of R-notebooks will introduce to to some of the neuroimaging data visualization tools R. You can work though these notebooks on RStudio Cloud, or locally on Rstudio. If you are using Rstudio cloud, or have github installed, clone this get repo by typing the following in to the terminal:
git clone https://github.com/sidchop/neuRo-vis-BrainHack-2021.git
We will go though how to visualize 4 different types of data:
-
Vertex-level data (Note: This note book will not work properly on RStudio Cloud due to space and RAM requirements. Also, visualisation will open in a new window (RGL graphics device), not within Rstudio)
You will need a basic understanding of R syntax. A understanding of R-Markdown syntax will be helpful, but not essential.
If you run into any problems while executing these notebooks of have any questions, please open an issue and describing the problem or question. You can also email me at sid.chopra@monash.edu.
If you are interested in plotting gifti and cifti data, check out:
- Voxel-level data: Thanks to John
Muschelli for developing
neurobaseand providing great documentation. - ROI-level data: Thanks to Athanasia
Mowinckel for developing
ggseg&ggseg3D, and her wonderful blog posts on how to use these packages. - Vertex-level data: Thanks to Tim Schäfer & Christine Ecker for developing fsbrain, a timely and much needed package.