BrainDynamics protocol

This protocol is based on our method: Varga, L. et al. Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture. Cell Systems, Volume 15, Issue 8, 770 - 786.e5 (2024). DOI: https://doi.org/10.1016/j.cels.2024.07.003

Requirements

• Python (tested for 3.12 and later versions)

  • igraph (0.11.6 or later)
  • pandas (2.2.2 or later)
  • scipy (1.14.0 or later)
  • matplotlib (3.9.2 or later)
  • cliffs_delta (1.0.0 or later)

• C/C++ compiler (e.g. gcc on Linux, Xcode Developer Tools for MacOS or Visual C++ Build Tools on Windows)

Setting up

1) Set up virtual python environment using python or conda.

For example:

python -m venv braindynamics_env

OR via Anaconda:

conda create --name braindynamics_env python=3.12

2) Install package from PyPi

 pip install braindynamics-starprotocol

3) Usage

For an example of the pipeline, check examples/pipeline_example.ipynb notebook, or run the .py file with the same name.

For more details, you can also refer to the documentation available on ReadTheDocs

Link to the PyPi project site for release history: https://pypi.org/project/braindynamics-starprotocol

4) Citation

Please cite our publication when using our code: Varga, L. et al. Protocol to study brain dynamics of mammals through the hierarchy of complex correlation patterns defining a robust functional architecture. STAR Protocols, Volume 6, Issue 2, 103693 (2025). DOI: https://doi.org/10.1016/j.xpro.2025.103693