ToMCAT Synchronize Physio Data

This project synchronizes EEG, EKG, GSR, fNIRS physio data and task data together under a unified time series.

Install dependencies

This project requires Python 3.11.

Install dependencies with Conda

Ensure that Conda is already installed, then run the following command to install dependencies into a new conda environment

conda conda create -n tomcat-synchronize python=3.11
conda activate tomcat-synchronize
pip install -r requirements.txt

Install dependcies with Pip

You can install the packages using Pip3 in a base environment or an environment created for this project, then run the follow command to install dependencies

pip3 install -r requirements.txt

Install dependencies manually

If you want to set up environment and install dependencies manually, then you need the following packages

pandas
numpy
scipy
scikit-learn
matplotlib
mne
tqdm

Set up project

Ensure that you downloaded the ToMCAT chunked data here, ToMCAT task data here, and ToMCAT experiment information here

Set the following variables in the config.py file:

• task_data_path is the full complete path to the ToMCAT task data you downloaded (make sure to decompress the data, e.g., unzip).
• physio_data_path is the full complete path to the ToMCAT chunked data you downloaded (make sure to decompress the data, e.g., unzip).
• experiment_info_path is the full complete path to the ToMCAT experiment information data you downloaded (make sure to decompress the data, e.g., unzip).
• output_dir is the full complete path to the output directory where the synchronized data will be placed.

Run project

After setting up the config.py file, you can launch the program (make sure that you are in the python environment with required dependencies installed):

Synchronize fNIRS with each task

python3 process_nirs.py

Synchronize EEG-EKG-GSR with each task

python3 process_nirs.py

Synchronize fNIRS-EEG-EKG-GSR together with each task

python3 process_nirs_eeg.py

Synchronize, low-pass filter, and downsample EEG-EKG-GSR to 120 Hz

python3 process_nirs_eeg_120 Hz.py

Output

The program will output synchronized data to the path specified in output_dir in config.py.