README.md

ReTune Invasive Electrophysiology Tutorial I

Provided by projects B03, C01 and INF

what you will learn:

Ephys tutorial 1 shows on an entry-level how ECOG and LFP data are organized. Topics covered are:

• how explore data you recieve
• rearrange data in readable format
• plot channels
• find the sample frequency
• interpret some information (Stimulation state, medication state, stimulator model) and where to store these
• rewrite channel names
• how to do rereferencing of the signal
• save your data in Matlab, FieldTrip or SPM readable format
• convert your data to BIDS format (brainvision)
• explore the data in Python and use mne

what you need:

MATLAB

For the first part, you will need Matlab2020b as we start with this script https://github.com/retune-commons/InvasiveElectrophysiologyWorkshop_I/blob/main/Tutorial_I_Import_and_rereference.m

The dependencies are:

• spm: https://github.com/spm/spm12
• wjn_toolbox: https://github.com/neuromodulation/wjn_toolbox
• FieldTrip: https://github.com/fieldtrip/fieldtrip.git
• MatLab Signal Processing Toolbox

Python

For the second part, you need jupyter notebook as we end the tutorial with this script https://github.com/retune-commons/InvasiveElectrophysiologyWorkshop_I/blob/main/Tutorial_1_import_and_rereferences.ipynbT

The dependencies are:

• mne tools https://mne.tools/stable/index.html, that can be installed using following command:

import sys
!{sys.executable} -m pip  install mne

We welcome your feedback on this tutorial. This tutorial is created by the Interventional and Cognitive Neuromodulation Lab: https://www.icneuromodulation.org/