https://github.com/coganlab/ieeg_pipelines

A repo of current preprocessing methods for the Cogan Lab
https://github.com/coganlab/ieeg_pipelines

bids-apps eeg ieeg matlab neuroscience python

Last synced: about 2 months ago
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A repo of current preprocessing methods for the Cogan Lab

• Host: GitHub
• URL: https://github.com/coganlab/ieeg_pipelines
• Owner: coganlab
• License: mit
• Created: 2021-05-10T16:08:13.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-10-25T19:10:25.000Z (about 2 months ago)
• Last Synced: 2024-10-26T20:07:25.211Z (about 2 months ago)
• Topics: bids-apps, eeg, ieeg, matlab, neuroscience, python
• Language: Python
• Homepage: https://ieeg-pipelines.readthedocs.io/en/latest/
• Size: 115 MB
• Stars: 4
• Watchers: 0
• Forks: 2
• Open Issues: 21
• Metadata Files:
  • Readme: README.md
  • Contributing: docs/contributing.rst
  • License: LICENSE

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README

        
# IEEG_Pipelines

A repo of current preprocessing pipelines for the [Cogan Lab](https://www.coganlab.org/)

[![Brain](./docs/images/brain_rot.gif)](https://www.coganlab.org/)

## Documentation

[![Documentation Status](https://readthedocs.org/projects/ieeg-pipelines/badge/?version=latest)](https://ieeg-pipelines.readthedocs.io/en/latest/?badge=latest)

[Lab Wiki](https://coganlab.pages.oit.duke.edu/wiki//)

## Pipeline Functionality

[![Python (3.10) on Windows/Linux](https://github.com/coganlab/IEEG_Pipelines/actions/workflows/Python-CI.yml/badge.svg)](https://github.com/coganlab/IEEG_Pipelines/actions/workflows/Python-CI.yml)

[![MATLAB latest](https://github.com/coganlab/IEEG_Pipelines/actions/workflows/MATLAB-CI.yml/badge.svg)](https://github.com/coganlab/IEEG_Pipelines/actions/workflows/MATLAB-CI.yml)

[![codecov](https://codecov.io/gh/coganlab/IEEG_Pipelines/branch/main/graph/badge.svg?token=X4IAFGOBGN)](https://codecov.io/gh/coganlab/IEEG_Pipelines)

## Installation

### MATLAB

1. Install MATLAB

2. Clone this repository into your userpath (`Documents/MATLAB` by default)

3. Run commands:

    ```MATLAB

    path = fullfile(userpath, 'IEEG_Pipelines', 'MATLAB');

    addpath(genpath(path));

    ```

### Python

Version 3.10 supported

#### Conda

1. Install Anaconda

2. Create an anaconda environment with python and pip packages installed

    

     ```bash

     conda create -n  python<3.13 pip

     ```

3. Activate the environment

    ```bash

    conda activate 

    ```

   

4. Run

    ```bash

    pip install ieeg

    ```

#### [Pip](https://pypi.org/project/ieeg/)

1. Install Python

2. Run:

    ```bash

    python -m venv /

    source activate /

    python -m pip install ieeg

    ```

   

## Usage

### MATLAB (INCOMPLETE)

1. Load `.dat` file using [convert_OpenE_rec2mat.m](MATLAB/ieeg%20file%20reading/convert_OpenE_rec2mat.m)

2. Create the ieeg data structure from the [ieegStructClass.m](MATLAB/ieegClassDefinition/ieegStructClass.m)

3. `TBD`

### Python ([INCOMPLETE](https://github.com/orgs/coganlab/projects/7))

1. Load BIDS files from BIDS directory using [`pybids`](https://bids-standard.github.io/pybids/)

    

    ```python

    from bids import BIDSLayout

    import ieeg

    layout = BIDSLayout()

    data = ieeg.io.raw_from_layout(layout)

    ```

2. [Perform line noise filtering](https://ieeg-pipelines.readthedocs.io/en/latest/auto_examples/plot_clean.html)

3. [Check Spectrograms](https://ieeg-pipelines.readthedocs.io/en/latest/auto_examples/plot_spectrograms.html)

4. [Plot the high gamma responses](https://ieeg-pipelines.readthedocs.io/en/latest/auto_examples/plot_HG.html)

5. [Run the cluster correction and permutation test](https://ieeg-pipelines.readthedocs.io/en/latest/auto_examples/plot_stats.html)