Tutorials

Starting a new study

    1. Create a new protocol

    2. Import the subject anatomy

    3. Explore the anatomy

Reviewing

    4. Channel file / MRI registration

    5. Continuous recordings

    6. Multiple windows

    7. Event markers

Pre-processing

    8. Stimulation delays

    9. Select files / Run processes

    10. Power spectrum / Frequency filters

    11. Bad channels

    12. Artifact detection

    13. Artifact cleaning with SSP

    14. Additional bad segments

Epoching and averaging

    15. Import epochs

    16. Average response

    17. Visual exploration

    18. Colormaps

    19. Clusters of sensors

Source modeling

    20. Head model

    21. Noise/data covariance

    22. Source estimation

    23. Scouts

Advanced processes

    24. Time-frequency

    25. Difference

    26. Statistics

    27. Workflows

    28. Scripting

Anatomy and registration

• Brainstorm coordinate systems

• MRI segmentation: CAT12, FreeSurfer,
  BrainSuite, BrainVISA, FastSurfer, CIVET

• Using the anatomy templates

• Warping the anatomy templates

• Group analysis: Subjects coregistration

• Digitize EEG electrodes and head shape

• Real-time head positioning (CTF MEG)

• Head motion detection (MEG)

Recordings

• Montage editor

• ICA analysis

• SSP cookbook

• Detect subject movements

• Synchronization with eye tracker

Scripting

• How to write your own process

• Export volume sources to SPM8/SPM12

• Export surface sources to SPM12

• Export raw data to BIDS format

Software

• Plugins

• MNE-Python

• How to cite Brainstorm

• Known bugs

• Export figures to Plotly

Source modeling

• Volume source estimation

• Deep cerebral structures

• Realistic head model: BEM with OpenMEEG

• Dipoles: Scanning and displaying

• Dipoles: FieldTrip dipole fitting

• Maximum entropy on the mean (MEM)

• Other beamforming methods

• Simulations

Finite Element Modeling

• Realistic head model: FEM with DUNEuro

• FEM mesh generation

• FEM tensors estimation

• FEM median nerve example

Signal processing

• Machine learning: Decoding / MVPA

• Phase-amplitude coupling: Method

• Phase-amplitude coupling: Example

• Partial Least Squares (PLS)

• Epileptogenic Zone Fingerprint

• FOOOF: Fitting Oscillations & One-Over-F

• SPRiNT: Spectral Param. Resolved in Time

Connectivity

• Functional connectivity

• Corticomuscular coherence

• Connectivity graphs

• Virtual fibers for connectivity

• Granger causality

• EEG and epilepsy

• SEEG epileptogenicity maps

• ECoG+sEEG epilepsy (BIDS)

• MEG visual: single subject (Elekta/BIDS)

• MEG visual: group study (Elekta/BIDS)

• MEG current phantom (CTF)

• MEG current phantom (Elekta)

• MEG resting state & OMEGA database (CTF)

• MEG corticomuscular coherence (CTF)

• MEG Human Connectome Project (4D)

• MEG median nerve (Elekta)

• MEG median nerve (Yokogawa)

• MEG median nerve (CTF)

• NIRS finger tapping

Single/multi-unit electrophysiology

Learn how to use Brainstorm for analyzing single/multi-unit electrophysiological data in a variety of preparations:

Background readings

These tutorial pages suppose you are comfortable with the basic concepts of MEG and EEG source imaging. If you're not, we encourage you to read some background information, which will quickly help you getting up to speed with this field:

• MEG for Human Electrophysiology and Imaging (Baillet S, Nature Neuroscience, 2017)

• Connectomics of Human Electrophysiology (Sadaghiani S, Brookes M, Baillet S, Neuroimage, 2022)

• Introduction to MEG (Medical College of Wisconsin)
  A non-technical overview of MEG and EEG, with an emphasis on source modeling.

• MEG: An Introduction to Methods
  Editors: P Hansen, M Kringelbach, R Salmelin, Oxford University Press, 2010, 448 pages.

• The Oxford Handbook of Social Neuroscience
  Editors: J Decety, JT Cacioppo, Oxford University Press, 2011, 1128 pages
  A draft version of the MEG chapter by Sylvain Baillet can be found here.

• Good practice for conducting and reporting MEG research, Gross et al, Neuroimage, 2013.

• Slides from a selection of educational courses: megcommunity.org

• We can also come and organize a training session at your institution, or visit us at the MNI.

Now you are well equipped to go through the software tutorial, Enjoy!