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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.

Get started

The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. In just a few hours, you will be introduced to the essential features of the application.

Starting a new study

1. Create a new protocol

2. Import the subject anatomy

3. Explore the anatomy

Reviewing and pre-processing

4. Channel file and coregistration MEG-MRI

5. Continuous recordings

6. Montage editor [Under construction]

7. ?Multiple windows [Under construction]

8. Event markers [Under construction]

9. Stimulation delays [Under construction]

10. Frequency filters [Under construction]

11. Bad channels [Under construction]

12. Artifact detection [Under construction]

13. Artifact cleaning with SSP [Under construction]

14. Additional bad segments [Under construction]

Epoching and averaging [Under construction]

15. Import epochs

16. Average response

17. Exploring the average response

18. 2D/3D topography

19. Colormaps

Source modeling [Under construction]

20. Head model

21. Noise covariance

22. Source estimation

23. Scouts

Advanced topics [Under construction]

24. Time-frequency

25. Statistics

26. Connectivity

27. Phase-amplitude coupling

28. Advanced scripting

29. Complete tutorial script

30. Summary

Complete analysis of other datasets

EEG and epilepsy
MEG auditory tutorial
MEG median nerve (CTF) [Under construction]
MEG median nerve (Yokogawa/KIT)
MEG median nerve (Elekta-Neuromag) [Under construction]
MEG resting state

Advanced tutorials

Anatomy and registration

Brainstorm coordinate systems
MRI segmentation: FreeSurfer, BrainVISA, BrainSuite, CIVET
Using the anatomy templates [Under construction]
Warping default anatomy
Group studies: Subjects coregistration
Group studies: Averaging
Digitize EEG electrodes and head shape
Real-time head positioning in the CTF MEG system

Graphical scripting

Source modeling

BEM with OpenMEEG
Volume source estimation
Computing and displaying dipoles
Beamforming methods [Under construction]
Maximum Entropy on the Mean (MEM) [Under construction]

Functional connectivity

Phase-amplitude coupling

Statistics

Other useful how-to's

How to cite Brainstorm in your publications
Known bugs
?MEG analysis guidelines for McGill

Examples

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

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!

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 1. [[Tutorials/ImportAnatomy|Import the subject anatomy]]
 1. [[Tutorials/ExploreAnatomy|Explore the anatomy]]
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-. [[Tutorials/ChannelFile|Coregistration MEG-MRI]]
 1. [[Tutorials/ReviewRaw|Continuous recordings]]  [Under construction]
 1. [[Tutorials/MontageEditor|Montage editor]]   [Under construction]
 1. [[Tutorials/Desktop|Multiple windows]]
 1. [[Tutorials/EventMarkers|Event markers]]
 1. [[Tutorials/StimDelays|Stimulation delays]]
 1. [[Tutorials/ArtifactsFilter|Frequency filters]]
 1. [[Tutorials/BadChannels|Bad channels]]
 1. [[Tutorials/ArtifactsDetect|Artifact detection]]
 1. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]]
 1. [[Tutorials/BadSegments|Additional bad segments]]
+<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>4. [[Tutorials/ChannelFile|Channel file and coregistration MEG-MRI]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>5. [[Tutorials/ReviewRaw|Continuous recordings]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>6. [[Tutorials/MontageEditor|Montage editor]]   [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>7. [[Tutorials/Desktop|Multiple windows]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>8. [[Tutorials/EventMarkers|Event markers]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>9. [[Tutorials/StimDelays|Stimulation delays]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>10. [[Tutorials/ArtifactsFilter|Frequency filters]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>11. [[Tutorials/BadChannels|Bad channels]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>12. [[Tutorials/ArtifactsDetect|Artifact detection]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>13.  [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>14.  [[Tutorials/BadSegments|Additional bad segments]]  [Under construction]
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-. [[Tutorials/Epoching|Import epochs]]
 1. [[Tutorials/Averaging|Average response]]
 1. [[Tutorials/ExploreRecordings|Exploring the average response]]
 1. 2D/3D topography
 1. [[Tutorials/Colormaps|Colormaps]]
+<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>15. [[Tutorials/Epoching|Import epochs]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>16. [[Tutorials/Averaging|Average response]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>17. [[Tutorials/ExploreRecordings|Exploring the average response]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>18. 2D/3D topography

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>19. [[Tutorials/Colormaps|Colormaps]]
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 1. [[Tutorials/NoiseCovariance|Noise covariance]]
 1. [[Tutorials/SourceEstimation|Source estimation]]
 1. [[Tutorials/Scouts|Scouts]]
+<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>20. [[Tutorials/HeadModel|Head model]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>21. [[Tutorials/NoiseCovariance|Noise covariance]]

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 1. [[Tutorials/Statistics|Statistics]]
 1. [[Tutorials/Connectivity|Connectivity]]
 1. Phase-amplitude coupling
 1. [[Tutorials/Scripting|Advanced scripting]]
 1. Complete tutorial script
 1. Summary
+<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>24. [[Tutorials/TimeFrequency|Time-frequency]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>25. [[Tutorials/Statistics|Statistics]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>26. [[Tutorials/Connectivity|Connectivity]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>27. Phase-amplitude coupling

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>28. [[Tutorials/Scripting|Advanced scripting]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>29. Complete tutorial script

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>30. Summary

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