Differences between revisions 27 and 185 (spanning 158 versions)

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. However, note that those pages are updated with the software, and cannot be kept as long term reference documentation.

?Brainstorm architecture
?First steps
?Importing individual anatomy
?Importing MEG recordings
?Exploring the recordings
?Head model
?Noise covariance
?Source estimation
?Scouts
?Graphical scripting
?Statistics
?Time-frequency

Advanced tutorials

Processing continuous recordings

?Review continuous recordings and edit markers
?Detect and remove artifacts
?Epoching and averaging

Other types of recordings

EEG and Epilepsy
Neuromag raw recordings

Anatomy and registration

Graphical scripting

?Description of all the processes
Full analysis with one script
?How to write your own process

Source modeling

BEM with OpenMEEG
Volumetric source estimation
?Dipole models from Neuromag's Xfit

Other useful how-to's

Examples

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

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-= Tutorials =
== Important notes ==
 * In all the tutorials, we will consider that you are working with the source distribution of Brainstorm, as it is the recommanded way to use this toolbox. If you are working with compiled binaries, some menus might be missing, but everything else should work the same way.
 * Before starting using Brainstorm with your own data, you should go through all the tutorials.
 * If you want a printed version of this documentation: open a tutorial, go to the menu on top of the page, select ''More actions > Print view'', print the page, click on the ''Back ''button of your browser, and go to next tutorial.
+= 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 [[mailto:brainstorm@sipi.usc.edu|email us]] if you would like to contribute.
-Line 7:
+Line 4:
-== Starting with Brainstorm ==
+== 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: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]],

 * Slides from a selection of educational courses at [[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]],

 * Reference books:
  * 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. However, note that those pages are updated with the software, and cannot be kept as long term reference documentation.

 1. [[Tutorials/BstFolders|Brainstorm architecture]]
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-. [[Tutorials/TutImportRecordings|Importing recordings]]
+. [[Tutorials/TutImportRecordings|Importing MEG recordings]]
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+Line 30:
-. [[Tutorials/TutHeadModel|Computing a head model]]
 1. [[Tutorials/TutNoiseCov|Computing a noise covariance matrix]]
+. [[Tutorials/TutHeadModel|Head model]]
 1. [[Tutorials/TutNoiseCov|Noise covariance]]
-Line 15:
+Line 33:
-. [[Tutorials/TutScouts|Scouts: cortical regions of interest]]
 1. [[Tutorials/TutProcesses|Processes: Graphical batching interface]]
+. [[Tutorials/TutScouts|Scouts]]
 1. [[Tutorials/TutProcesses|Graphical scripting]]
 1. [[Tutorials/TutStat|Statistics]]
 1. [[Tutorials/TutTimefreq|Time-frequency]]
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+Line 38:
-== Other useful tutorials ==
 1. [[CiteBrainstorm|Cite Brainstorm in your publications]]
+== Advanced tutorials ==
=== Processing continuous recordings ===
 1. [[Tutorials/TutRawViewer|Review continuous recordings and edit markers]]
 1. [[Tutorials/TutRawSsp|Detect and remove artifacts]]
 1. [[Tutorials/TutRawAvg|Epoching and averaging]]

=== Other types of recordings ===
 1. EEG and Epilepsy
 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]]

=== Anatomy and registration ===
 1. [[CoordinateSystems|Brainstorm coordinate systems]]
 1. [[Tutorials/LabelFreeSurfer|MRI segmentation: FreeSurfer]]
 1. [[Tutorials/SegBrainVisa|MRI segmentation: BrainVISA]]

 1. [[Tutorials/TutWarping|Warping default anatomy]]

 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]]

=== Graphical scripting ===
 1. [[Tutorials/RefProcesses|Description of all the processes]]
 1. [[Tutorials/TutRawScript|Full analysis with one script]]
 1. [[RefWriteProcess|How to write your own process]]

=== Source modeling ===
 1. [[Tutorials/TutBem|BEM with OpenMEEG]]

 1. [[Tutorials/TutVolSource|Volumetric source estimation]]

 1. [[Tutorials/TutXfit|Dipole models from Neuromag's Xfit]]

=== Other useful how-to's ===
 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]]
 1. [[CoordinateSystems|Coordinate systems]]

 1. [[Tutorials/KnownBugs|Known bugs]]

=== Examples ===

 1. This video illustrate how Brainstorm can be used for studying amygdala activity:<<BR>>Balderston NL, Schultz DH, Baillet S, Helmstetter FJ<<BR>>[[http://www.jove.com/video/50212/how-to-detect-amygdala-activity-with-magnetoencephalography-using?status=a52218k|How to Detect Amygdala Activity with Magnetoencephalography using Source Imaging]]

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