A repo of current preprocessing pipelines for the Cogan Lab
-
Install MATLAB
-
Clone this repository into your userpath (
Documents/MATLAB
by default) -
Run commands:
path = fullfile(userpath, 'IEEG_Pipelines', 'MATLAB'); addpath(genpath(path));
Version 3.10 supported
-
Install Anaconda
-
Clone this repository
-
Open a terminal and
cd
into this repo'sPython
directory -
Run this command:
conda env create -f envs/environment.yml
-
When it is finished installing run
conda activate preprocess
to activate the environment
-
Install Python
-
Clone this repository
-
Open a terminal and
cd
into this repo'sPython
directory -
Run:
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
- Load
.dat
file using convert_OpenE_rec2mat.m - Create 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)