Tutorials

These tutorial pages suppose you are comfortable with the basic concepts of MEG/EEG analysis and source imaging. If you're not, we encourage you to read some background literature.
To get a quick overview of the software interface, you can watch this introduction video.
If you are looking for the old tutorials, they are still available ?here.

Get started

The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. The number between brackets represents the number of printed pages for each tutorial.
Some sections are still being edited or under review: Editing process.

Starting a new study     1. Create a new protocol [9]     2. Import the subject anatomy [8]     3. Explore the anatomy [13] Reviewing     4. Channel file / MRI registration [11]     5. Continuous recordings [9]     6. Multiple windows [5]     7. Event markers [10] Pre-processing     8. Stimulation delays [9]     9. Select files / Run processes [11]     10. Power spectrum / Frequency filters [15]     11. Bad channels [6]     12. Artifact detection [8]     13. Artifact cleaning with SSP [16]     14. Additional bad segments [7]

Epoching and averaging     15. Import epochs [9]     16. Average response [7]     17. Visual exploration [10]     18. Colormaps [5]     19. Clusters of sensors [4] Source modeling     20. Head model [9]     21. Noise/data covariance [7]     22. Source estimation [28]     23. Scouts [17] Advanced processing     24. Time-frequency [33]     25. Difference [13]     26. Statistics [30]     27. Workflows [Under construction]     28. Scripting [Under construction]

Other analysis scenarios

1. EEG and epilepsy

2. MEG auditory tutorial (CTF)

3. MEG median nerve (CTF) [Under construction]

4. MEG median nerve (Yokogawa)

5. MEG median nerve (Elekta) [Under construction]

6. MEG resting state (CTF)

7. MEG visual single subject (Elekta) [Under construction]

8. MEG visual group study (Elekta) [Under construction]

9. MEG current phantom (CTF)

10. MEG current phantom (Elekta)

11. NIRS finger tapping

Advanced tutorials

Recordings

1. Montage editor [Under construction]

2. ?ICA decomposition [Under construction]

3. Cleaning artifacts using SSP: examples

4. Detect subject movements

5. Real-time head-tracking for adjusting head position

6. Synchronization with eye tracker

Anatomy and registration

1. Brainstorm coordinate systems

2. MRI segmentation: FreeSurfer, BrainSuite, BrainVISA, CIVET

3. Using the anatomy templates

4. Warping default anatomy

5. Group analysis: Subjects coregistration

6. Digitize EEG electrodes and head shape

7. Real-time head positioning in the CTF MEG system

Source modeling

1. BEM with OpenMEEG

2. Volume source estimation

3. Deep cerebral structures [Under construction]

4. Computing and displaying dipoles

5. Dipole fitting with FieldTrip

6. Beamforming methods [Under construction]

7. Maximum Entropy on the Mean (MEM)

8. Maximum Entropy on the Mean (MEM) - Epilepsy

Advanced processing

1. Functional connectivity [Under construction]

2. Phase-amplitude coupling

3. Export volume source maps to SPM8 / SPM12

4. Export surface source maps to SPM12

5. Decoding conditions (MVPA)

6. Microstate segmentation with CENA

7. How to write your own process

Other useful how-to's

1. ?Brainstorm on IPython Notebook [Under construction]

2. How to cite Brainstorm in your publications

3. Known bugs

4. All the introduction tutorials on the same page

Tutorials from other authors

1. This video illustrates how Brainstorm can be used for studying amygdala activity:
   How to Detect Amygdala Activity with Magnetoencephalography using Source Imaging
   Authors: Balderston NL, Schultz DH, Baillet S, Helmstetter FJ

2. A tutorial in Japanese (click on the menu "Brainstorm")

3. ?MEG analysis guidelines for McGill

Background readings

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

• A non-technical overview of MEG and EEG, with an emphasis on source modeling:
  Canada MEG Consortium

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

• Reference books:

  • 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

• You can also ask us to come and organize a training session at your institution, or visit us to obtain training (McGill's Montreal Neurological Institute).

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