Welcome to the IEEG_Pipelines Documentation¶
This is the main page of the IEEG_Pipelines documentation. Here you will find the table of contents and links to other important resources.
IEEG_Pipelines¶
A repo of current preprocessing pipelines for the Cogan Lab
Documentation¶
Pipeline Functionality¶
Installation¶
MATLAB¶
Install MATLAB
Clone this repository into your userpath (
Documents/MATLAB
by default)Run commands:
path = fullfile(userpath, 'IEEG_Pipelines', 'MATLAB'); addpath(genpath(path));
Python¶
Version 3.10 supported
Conda¶
Install Anaconda
Clone this repository
Open a terminal and
cd
into this repo’sPython
directoryRun this command:
conda env create -f envs/environment.yml
When it is finished installing run
conda activate preprocess
to activate the environment
Pip¶
Install Python
Clone this repository
Open a terminal and
cd
into this repo’sPython
directoryRun:
python -m venv <PATH TO VENV>/preprocess python -m pip install -r envs/requirements.txt -e <PATH TO VENV>/preprocess
When it is finished installing run
source activate <PATH TO VENV>/preprocess
to activate the environment
Usage¶
MATLAB (INCOMPLETE)¶
Load
.dat
file using convert_OpenE_rec2mat.mCreate the ieeg data structure from the ieegStructClass.m
TBD
Python (INCOMPLETE)¶
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)
Indices and Tables¶
Thank you for using IEEG_Pipelines!