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Brainstorm Tutorials

The following pages will take you through a typical workflow of data analyses that will feature most of the tools and applications of Brainstorm. We are updating these pages constantly, keeping up with new developments and features in the software.

You are therefore welcome to suggest improvements and additions but also to contribute by becoming an editor of this wiki. Please email us if you would like to contribute.

Required background

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: here,
Slides from a selection of educational courses at megcommunity.org,
Reference books:
- Peter Hansen, Morten Kringelbach, and Riitta Salmelin (Eds)
  MEG: An Introduction to Methods, Oxford University Press, (29 July 2010), 448 pages, ISBN-13: 978-0195307238
- Jean Decety & John T. Cacioppo (Eds)
  The Oxford Handbook of Social Neuroscience, Oxford University Press, (Sept 2011), 1128 pages, ISBN-10: 019534216X.
  A draft version of the MEG chapter by Sylvain Baillet can be found here.
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!

Get started: 12 easy steps through Brainstorm

The easiest way to get started with Brainstorm is to follow carefully those 12 introduction tutorials. In just a few hours, you will be introduced to the essential features of the application.

If you need a printed version of a page, click on the "print" link at the top-right corner of the page.

?0. Brainstorm architecture
?1. First steps
?2. Importing individual anatomy
?3. Importing MEG recordings
?4. Exploring the recordings
?5. Head model
?6. Noise covariance
?7. Source estimation
?8. Scouts: Cortical regions of interest
?9. Processes: Graphical batching interface
?10. Statistics
?11. Time-frequency

Advanced tutorials

Processing continuous recordings

?Review raw recordings and edit markers
Import and process raw recordings
Automated processing: a full analysis as a script

Anatomy and registration

Source modeling

Boundary Element Modeling (BEM)
Source estimation not constrained to cortical surface
?Import and visualize dipole models from another software (Neuromag's Xfit)
?BrainEntropy MEM (Maximum Entropy on the Mean)

Other useful how-to's

How to cite Brainstorm in your publications
?How to use Brainstorm without the GUI
?How to compile Brainstorm
Known bugs

Get started (details)

?0. Brainstorm architecture
?1. First steps
?2. Importing individual anatomy
?3. Importing MEG recordings
?4. Exploring the recordings
?5. Computing a head model
?6. Computing a noise covariance matrix
- Compute from recordings
- Noise covariance from another dataset
?7. Source estimation
?8. Scouts: Cortical regions of interest
?9. Processes: Graphical batching interface
?10. Statistics
?11. Time-frequency

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-= Tutorials =
The following pages will take you through a typical workflow of data analyses that will feature most of the tools and applications of Brainstorm. We are updating these pages constantly, keeping up with new developments and features in the software: you are therefore welcome to [[mailto:brainstorm@sipi.usc.edu|suggest]] improvements and additions but also to contribute by becoming a editor of this wiki. Please [[mailto:brainstorm@sipi.usc.edu|email us]] if you would like to contribute.
+= Brainstorm Tutorials =
The following pages will take you through a typical workflow of data analyses that will feature most of the tools and applications of Brainstorm. We are updating these pages constantly, keeping up with new developments and features in the software.

You are therefore welcome to [[mailto:brainstorm@sipi.usc.edu|suggest]] improvements and additions but also to contribute by becoming an editor of this wiki. Please [[mailto:brainstorm@sipi.usc.edu|email us]] if you would like to contribute.

== Required background ==
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- * Non-technical overview of MEG and EEG, with an emphasis on source modeling and imaging: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]],
+ * A non-technical overview of MEG and EEG, with an emphasis on source modeling: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]],
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- . * Peter Hansen, Morten Kringelbach, and Riitta Salmelin (Eds)
 [[http://www.amazon.com/MEG-Introduction-Methods-Peter-Hansen/dp/0195307232/ref=sr_1_1?ie=UTF8&qid=1324419425&sr=8-1|MEG: An Introduction to Methods]] Oxford University Press;  (29 July 2010); 448 pages; ISBN-13: 978-0195307238
  . * The following book features an extensive introduction to MEG:
  . * [[http://www.amazon.com/Oxford-Handbook-Neuroscience-Library-Psychology/dp/019534216X/ref=sr_1_3?s=books&ie=UTF8&qid=1324419480&sr=1-3|The Oxford Handbook of Social Neuroscience]] (Oxford Library of Psychology), (Sept 2011) Jean Decety (Editor), John T. Cacioppo (Editor), ISBN-10: 019534216X, 1128 pages.
  . * A draft version of the chapter can be found here.

== Tutorial Guidelines ==
 1. Go through the 12 steps of ''Getting started with Brainstorm'' (see below). In just a few hours, you will be introduced to the essential features of the application.
 1. Read more specific tutorials (see ''Advanced Tutorials'' below), related to your personal interests/needs.
 1. If you need a printed version of a page, click on the "print" link at the top-right corner of the page.

== 12 easy steps through Brainstorm ==
+  * Peter Hansen, Morten Kringelbach, and Riitta Salmelin (Eds)<<BR>>[[http://www.amazon.com/MEG-Introduction-Methods-Peter-Hansen/dp/0195307232/ref=sr_1_1?ie=UTF8&qid=1324419425&sr=8-1|MEG: An Introduction to Methods]], ''Oxford University Press'',  (29 July 2010), 448 pages, ISBN-13: 978-0195307238

  * Jean Decety & John T. Cacioppo (Eds)<<BR>>[[http://www.amazon.com/Oxford-Handbook-Neuroscience-Library-Psychology/dp/019534216X/ref=sr_1_3?s=books&ie=UTF8&qid=1324419480&sr=1-3|The Oxford Handbook of Social Neuroscience]]'', Oxford University Press'', (Sept 2011), 1128 pages, ISBN-10: 019534216X.<<BR>>A draft version of the MEG chapter by Sylvain Baillet can be found [[attachment:BailletMEGDraft.pdf|here]].

 * You can also ask us to come and organize a [[Training|training session]] at your institution, or [[http://www.bic.mni.mcgill.ca/ResearchLabsNeuroSPEED/HomePage|visit us]] to obtain training (!McGill's  Montreal Neurological Institute).

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

== Get started: 12 easy steps through Brainstorm ==
The easiest way to get started with Brainstorm is to follow carefully those 12 introduction tutorials. In  just a few hours, you will be introduced to the essential features of  the application.

If you need a printed version of a page, click on the "print" link at the top-right corner of the page.
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- * [[Tutorials/TutHeadModel|5. Computing a head model]]
 * [[Tutorials/TutNoiseCov|6. Computing a noise covariance matrix]]
+ * [[Tutorials/TutHeadModel|5. Head model]]
 * [[Tutorials/TutNoiseCov|6. Noise covariance]]
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-=== Exploring Continuous Recordings ===
+=== Processing continuous recordings ===
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+. [[Tutorials/TutFullAnalysis|Automated processing: a full analysis as a script]]
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-. [[Tutorials/SegBrainSuite|MRI segmentation with BrainSuite]]
+. [[Tutorials/LabelFreeSurfer|FreeSurfer cortical parcellation]]
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+. [[Tutorials/TutDigitize|Digitize EEG electrodes locations and head shape]]
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Software

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