Key Features:
- Uses modern browsers, easy to embed and share
- Displays MRI, surfaces, and electrodes in the same canvas
-
Maps multiple subjects on template brains using
AFNI/SUMA
(standard 141) orMNI-305
locations - Electrode localization in 3 approaches
- Volume rendering and surface/electrode animation
- Integration with interactive
R-shiny
framework
News | reference page | keyboard shortcuts
System Requirement
-
Web Browsers: the viewer uses
WegGL2
to render in browsers. Please check this list to see compatible browsers. As of 2023, Chrome, Firefox, Safari, and Edge (not IE) have full supports.
A. Installation
-
R
andRStudio Desktop (Free Version)
- Open
RStudio
, enter from its console:
install.packages("threeBrain")
If you want to install dev
version from Github, then use:
install.packages("remotes")
remotes::install_github("dipterix/threeBrain")
- (Optional) Setups: after installation, in
RStudio
console, type the following command
threeBrain::brain_setup()
and follow the instructions.
B. Basic Brain Viewer
Once finishing setting up of threeBrain
, there will be a template subject N27
(Collin’s 27) created locally. The location is platform-related. You can find it by running the following command:
library(threeBrain)
default_template_directory()
#> [1] "/Users/dipterix/Library/Application Support/
#> org.R-project.R/R/threeBrain/templates"
N27 template folder resides inside of this directory.
Let’s view this subject using the freesurfer_brain2
function.
- Import subject
library(threeBrain)
n27_path <- file.path(default_template_directory(), "N27")
x <- freesurfer_brain2( fs_subject_folder = n27_path,
subject_name = 'N27', surface_types = 'pial')
- Visualize
plot(x) # alternatively, you can use `n27$plot()`
C. Subject Setup
The sample subject (N27
) is a sample generated by FreeSurfer
(download). If you have any subjects processed by FreeSurfer
, use function freesurfer_brain2
to visualize.
D. Add/Render Electrodes
If you have electrode file, you can import it before calling plot
function. Please make sure it’s in csv
format.
x$set_electrodes(electrodes = "[PATH to ELECTRODE FILE]")
Here is an example of electrode csv file. Only the first five columns (case-sensitive) are mandatory: Electrode (integer)
, Coord_x
, Coord_y
, Coord_z
, and Label (character)
. Coord_*
is tkRAS
location from FreeSurfer
coordinates.
| Electrode| Coord_x| Coord_y| Coord_z|Label | MNI305_x| MNI305_y| MNI305_z|SurfaceElectrode |SurfaceType | Radius| VertexNumber|Hemisphere |
|---------:|-------:|-------:|-------:|:------|--------:|---------:|---------:|:----------------|:-----------|------:|------------:|:----------|
| 1| 29.0| -7.8| -34.6|RMHCH1 | 30.46817| -17.98119| -23.40022|FALSE |pial | 2| -1|left |
| 2| 33.8| -8.0| -34.2|RMHCH2 | 35.57109| -17.76624| -22.80131|FALSE |pial | 2| -1|left |
| 3| 38.0| -7.5| -33.5|RMHCH3 | 39.97102| -16.81249| -22.17986|FALSE |white | 2| -1|right |
| 4| 42.6| -6.8| -33.0|RMHCH4 | 44.79092| -15.73442| -21.82591|FALSE |smoothwm | 2| -1|right |
| 5| 47.0| -6.8| -32.6|RMHCH5 | 49.45370| -15.35431| -21.31272|FALSE |pial | 2| -1|right |
| ...
To assign values to electrodes, run
x$set_electrode_values(electrodes = "[PATH to ELECTRODE VALUE FILE]")
The electrode value file is also a csv like:
| Electrode| Subject| Project| Time| ValueName| ValueName2| ...|
|---------:|-------:|-------:|-------:|:---------|----------:|-----|
| 1| N27| Demo| 0|A | 30.46817| ...|
| 2| N27| Demo| 0|B | 35.57109| ...|
| 3| N27| Demo| 0|C | 39.97102| ...|
| 4| N27| Demo| 0|D | 44.79092| ...|
| 5| N27| Demo| 0|A | 49.45370| ...|
| ...
Project
and Time
are optional. However, if you are also using rave
, please make sure Project
exists. If you want to show animation, Time
is necessary and must be numeric. ValueName?
can be any characters containing letters (A-Z
, a-z
), letters (0-9
) and underscore (_
).
E. Merge Subjects and Template mapping
If you have your own subjects with FreeSurfer
output, for example, I have two subjects YAB
and YCQ
. To merge these two subjects and show them on N27
template,
library(threeBrain)
# yab = ... (see section B for import a single subject)
# ycq = ...
template_n27 = merge_brain(yab, ycq, template_subject = 'N27')
plot( template_n27 )
The viewer will be in N27
template, and electrodes of these two subjects can be mapped via MNI305
(for surface and stereo EEG) or std.141
(for surface-only).
F. Electrode Localization (YAEL
)
YAEL
: “Yet Another Electrode Localization” is a module that has been integrated into RAVE (R Analysis and Visualization of iEEG). The paper will come out soon. Please contact RAVE team on how to localize electrodes.
Citation
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.
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},
}
License
This package as a whole is licensed under GPL-3.0. The front-end viewer does not contain GNU components.
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.