A preliminary implementation of BrainGNN. The example presented here is on the public resting-state fMRI ABIDE for the convenience of development. This dataset was different from the ones used in our publication, which are cleaner task-fMRI. Still seeking solutions improve representation learning on the noisy data.
pip
See the requirements.txt for environment configuration.
pip install -r requirements.txtPYG
To install pyg library, please refer to the document
ABIDE
We treat each fMRI as a brain graph. How to download and construct the graphs?
python 01-fetch_data.py
python 02-process_data.py
Training and testing are integrated in file main.py. To run
python 03-main.py
If you find the code and dataset useful, please cite our paper.
@article{li2020braingnn,
title={Braingnn: Interpretable brain graph neural network for fmri analysis},
author={Li, Xiaoxiao and Zhou,Yuan and Dvornek, Nicha and Zhang, Muhan and Gao, Siyuan and Zhuang, Juntang and Scheinost, Dustin and Staib, Lawrence and Ventola, Pamela and Duncan, James},
journal={bioRxiv},
year={2020},
publisher={Cold Spring Harbor Laboratory}
}