WebGL-based 3D Brain for Python
The project is part of YAEL.
Installation
pypi
:
Install from # Bare minimal
pip install threebrainpy
# to allow Jupyter support
pip install threebrainpy threebrainpywidget
Github
:
Install from pip install pandas matplotlib
pip install git+https://github.com/dipterix/threebrainpy
Test the installation
Launch Python with your favorite editor, run the following Python commands. If you don't have FreeSurfer
installed, replace path
with any fs subject. If you don't have any, go to sample templates and download one.
import os
from threebrainpy.core import Brain
# You can replace `path` with any FreeSurfer-generated subject folder
path = os.path.join(os.environ["FREESURFER_HOME"], "subjects", "fsaverage")
brain = Brain(os.path.basename(path), path)
brain.add_slice("brain")
brain.add_slice("brain.finalsurf")
brain.add_surfaces("pial")
brain.render()
Documentation
Please check the documentation here.
Other implementations
This Python package implements the core functionalities. More advanced features will come soon.
The core script is written in JavaScript. The R implementation threeBrain is available on CRAN.
Here is a comparison of the Python vs R packages:
Feature | R | Python |
---|---|---|
3D Brain | â | â |
3D Electrodes | â | â |
Electrode Localization | â | â¤ï¸ |
Dashboard Integration | â | â¤ï¸ |
- â = implemented
- â¤ï¸ = will implement if I get enough requests or I get grants to do so
Sponsor
There has been no sponsor in this Python project yet. It is super hard and discouraging for software projects to apply for fundings. Your support will be greatly appreciated. Please email help
at rave.wiki
to join our slack channel if you want to:
- Request a demos
- Ask questions
- Use our software
- Collaborate with us