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Python

Installation

Installing conda

If you don't have python, we recommand to install it using conda. Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux. Conda quickly installs, runs, and updates packages and their dependencies. Conda easily creates, saves, loads, and switches between environments on your local computer.

For a quick and light installation, We recommand to use miniconda a free minimal installer for conda.

Select the version corresponding to your operating system and download and install it.

Create a new environment

[Windows user]

Once completed, you should have access to a new shell named Anaconda Prompt on your computer. Next instructions assume that your are using this shell.

[MacOS/Linux user]

Use your usual terminal (bash).

Launch your terminal and create a new python environment using the conda create command.

conda create -n bh_epilepsy python=3.9

Here we specify the name of the new environment bh_epilepsy and the python version 3.9.

Anaconda will ask you if you are sure you can to create this new environment

Proceed ([y]/n)?

Press y (yes) then Enter to accept

Installing dependencies

Activate the new environment using:

conda activate bh_epilepsy

Notice that the current environment is displayed at the beginning of your shell:

(bh_epilepsy) C:\Users\user_name>

Install the required python packages:

  • notebook to use jupyter notebook interface:

    pip install notebook

  • mne the main python EEG librairy.

    pip install mne

  • mne-qt-browser a 2D backend for plotting MNE data.

    pip install PyQt5 mne-qt-browser

  • pycartool to read EEG file fro Cartool.

    pip install git+https://github.com/Functional-Brain-Mapping-Laboratory/PyCartool

  • pandas library to work with dataframes

    pip install pandas

  • scikit learn a library to do machine learning with python.

    pip install -U scikit-learn

  • umap-learn a library to do machine learning with python

    pip install umap-learn

Use

Each time you want to use the environment, you need to activate it using:

conda activate bh_epilepsy

Then start the jupyter server:

jupyter notebook

To set mne-qt-browser as your default EEG viewer, edit your mne config:

import mne
mne.set_config('MNE_BROWSER_BACKEND', 'qt')