IEEG_Pipelines

A repo of current preprocessing pipelines for the Cogan Lab

Documentation

Lab Wiki

Pipeline Functionality

Installation

MATLAB

1. Install MATLAB

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

3. Run commands:

   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

   conda create -n <YOUR_NAME> python<3.13 pip

3. Activate the environment

   conda activate <YOUR_NAME>

4. Run

   pip install ieeg

Pip

1. Install Python

2. Run:

   python -m venv <PATH TO VENV>/<YOUR_NAME>
   source activate <PATH TO VENV>/<YOUR_NAME>
   python -m pip install ieeg

Usage

MATLAB (INCOMPLETE)

1. Load .dat file using convert_OpenE_rec2mat.m
2. Create the ieeg data structure from the ieegStructClass.m
3. TBD

Python (INCOMPLETE)

1. Load BIDS files from BIDS directory using pybids

   from bids import BIDSLayout
   import ieeg
   layout = BIDSLayout(<BIDS_root>)
   data = ieeg.io.raw_from_layout(layout)

2. Perform line noise filtering

3. Check Spectrograms

4. Plot the high gamma responses

5. Run the cluster correction and permutation test