Imaging in Neuroscience: with a focus on MEG and EEG Methods

Here you find the tutorials for the doctoral course Imaging in Neuroscience: with a focus on MEG and EEG Methods at Karolinska Institutet from April 14th to May 3rd.

This is an attempt to port from MATLAB to MNE-python.

All tutorials are example of how to analyse MEG/EEG signals. This is not meant as an exhaustive account of how to analyse MEG/EEG data. The material is design to give an overview of different aspects of MEG/EEG data analysis and useable example code on how to do the analysis.

To run the tutorial you need MNE-Python (https://mne.tools/stable/index.html), for that you first need to install Python and some modules, preferably installed in an Anaconda virtual environment.

For this course, you will use the module MNE-python and its dependencies to analyses MEG/EEG data. It is recommended that you also install Anaconda, a virtual envorinment.

Follow the instructions on how to install Anaconda and MNE here

You also need the tutorial data. All tutorials use MNE-Python. To learn more about MNE-Python, we recommend looking at the MNE-Python webpage for documentation and many more tutorial examples.

Here the scripts are written in Spyder, an envirornmet that is well suited for our purposes and will make any transition from MATLAB to Python easier.

Overview

The tutorial for the course is divided in seven parts numbered 01-07. Each part consist of one or more pages:

• tutorial_01a_preprocessing

• tutorial_01b_evoked responses

• tutorial_02_frequencyanalysis

• tutorial_03_prepare_mri

• tutorial_04a_dipole analysis

• tutorial_04b_mne

• tutorial_05_beamformer

• tutorial_06_connectivity

• tutorial_07_statistics

In addition, there is extra tutorials that are not part of the main assignment. They contain tips for writing analysis scripts and example on how to create surface-based source models with Freesurfer (www.freesurfer.net) and import them to FieldTrip

• tutorial_00_tips_for_writing_scripts
• tutorial_99_prepare_mne_sourcespace

Exam and questions

Thought the tutorials you will find questions like this:

Question X.X: what is an ERP?

For the course Imaging in Neuroscience: with a focus on MEG and EEG Methods your assignment is to answer the questions in a separate text document and submit through Canvas. When you answer the questions, use examples, code, and figures from the exercises.

Credits

All material is free to use under general license.

The tutorial material is created 2018-2020 by

• Mikkel C. Vinding, NatMEG, Karolinska Insitutet.
• Lau M. Andersen, CFIN, Aarhus University (www.laumollerandersen.org/).
• Robert Oostenveld, Donders Institute for Brain, Cognition and Behaviour, Radboud University.

The attempt to port the tutorials to MNE-Python was done by Andreas Gerhardsson

If you discover errors in the tutorials, code that won't run, or similar, please post your errors to: andreas.gerhardsson@ki.se