BCGNet is a deep learning toolbox based on Keras and TensorFlow for ballistocardiogram (BCG) artifact reduction. More detail about our model and methods can be found here.
Before setting up the Python environment, there might be several additional software dependencies that need to be installed if the user wishes to use the GPU version of TensorFlow for training, which is must faster than the CPU version. Please note GPU version of TensorFlow is available only for compatible GPUs from NVIDIA.
For the Tensorflow version 2.3.0 we used for testing this package, NVIDIA driver version has to be at least 418.39 and CUDA version has to be 10.1. Our build was tested using NVIDIA driver version 435.21 and CUDA 10.1.
To install NVIDIA driver, download the desired version for the particular OS and GPU on your local unit under the 'Advanced Driver Search' here.
To install CUDA, detailed instructions can be found here.
Note: after installing, NVIDIA driver and CUDA version can be checked by executing nvidia-smi in your terminal.
Once CUDA is successfully installed, the user can proceed to install CuDNN. Detailed instructions for installing CuDNN
can be found here.
Note: For Linux users, note that it's critical that LD_LIBRARY_PATH, which maps the CuDNN path, is added to
.bashrc and sourced.
It's recommended to install either anaconda or the lightweight miniconda on your machine for managing the Python
environment. To install anaconda/miniconda, detailed instructions can be found here.
The recommended way is to set up a new conda environment using the requirement.yml file we provide. Alternatively,
the user can choose to install all the packages using pip.
First clone/download our package into any directory you wish, then set up the dependencies via the following ways.
To set up the environment using the yml file, simply execute the following commands, and a new conda environment with
name bcgnet_TF230
cd $PATH_TO_OUR_PACKAGE
conda env create -f requirement.yml
Alternatively, the user can choose to install all the Python dependencies using pip via the following commands
cd $PATH_TO_OUR_PACKAGE
pip install requirement.txt
The user then needs to install jupyterlab and the detailed instructions can be found here.
Note: to check the TensorFlow version, execute
python -c 'import tensorflow as tf; print(tf.__version__)'
Once the package is downloaded and all dependencies are installed, the user can learn sample usage
in demo.ipynb, which uses two runs of data from a single subject. To do that, the user type the following in
their terminal
conda activate bcgnet_TF230
jupyter lab
and then open up the demo file in the browser window.
The directory structure is as follows
BCGNet
|-config
| __init__
| default_config.yaml
| load_config
|-dataset
| __init__
| dataset_utils
| default_dataset
|-example_data
|-models
| __init__
| default_models
| gru_arch_000
| model_utils
|-session
| __init__
| data_generator
| default_session
|-utils
| __init__
| context_management
|-.gitignore
|-__init__
|-demo.ipynb
|-README.md
|-requirement.txt
|-requirement.yml
In particular \config contains the configuration file default_config.yaml as well as the python functions that
handles loading of configuration files in load_config.py.
\dataset contains functions that handles single runs of data, which are encapsulated in dataset objects defined in
default_datasets.py while some utility functions are in dataset_utils.py.
\example_data contains two runs of raw data and the same runs of data processed by the optimal basis set (OBS)
method.
\models contains the neural network models that are used. The model from our paper is defined in
default_models.py and gru_arch_000 provides an example for user on how to define a custom model. Please note that
each model must be contained in a separate file with the name of the file same as the name of the model.
model_utils.py handles loading of the models.
\session contains functions that handles the entire training session, defined in default_session.py while
data_generator.py defines the data generator for training the models.
\utils contains utility functions that are used for the entire project.
If you use this code in your project, please cite:
McIntosh, J. R., Yao, J., Hong, L., Faller, J., & Sajda, P. (2020). Ballistocardiogram artifact
reduction in simultaneous EEG-fMRI using deep learning. IEEE Transactions on Biomedical
Engineering.
Direct link: https://ieeexplore.ieee.org/document/9124646
Bibtex format:
@article{mcintosh2020ballistocardiogram,
title={Ballistocardiogram artifact reduction in simultaneous EEG-fMRI using deep learning},
author={McIntosh, James R and Yao, Jiaang and Hong, Linbi and Faller, Josef and Sajda, Paul},
journal={IEEE Transactions on Biomedical Engineering},
year={2020},
publisher={IEEE}
}
