Differences between revisions 191 and 283 (spanning 92 versions)

Tutorials [2011-2014]

[WARNING: This page is part of the old tutorials, please refer to the new documentation]

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:
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!

Get started

The easiest way to get started with Brainstorm is to follow carefully these introduction tutorials. In just a few hours, you will be introduced to the essential features of the application. You will find a report form at the end of each tutorial, please share your comments to help us improve the documentation and the software. To get a quick overview of the software interface, you can watch this introduction video.

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 these pages are updated with the software, and cannot be kept as long term reference documentation.

12 easy steps through Brainstorm

?Brainstorm architecture [10 min]
?First steps [30 min]
?Importing individual anatomy [30 min]
?Importing MEG recordings [30 min]
?Exploring the recordings [60 min]
?Head model [30 min]
?Noise covariance [30 min]
?Source estimation [45 min]
?Scouts [45 min]
?Graphical scripting [45 min]
?Statistics [30 min]
?Time-frequency [1:30 hr]

Processing continuous recordings

?Review continuous recordings and edit markers [2:00 hr]
?Detect and remove artifacts [2:00 hr]
?Epoching and averaging [1:30 hr]

Advanced tutorials

Complete analysis of other datasets

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

Anatomy and registration

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
Cleaning artifacts using SSP: examples
?Detecting bad segments in continuous recordings
Detect subject movements
Real-time head-tracking for adjusting head position
A tutorial in Japanese (click on the menu "Brainstorm")

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

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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 [[mailto:brainstorm@sipi.usc.edu|email us]] if you would like to contribute.
+= Tutorials [2011-2014] =
'''[WARNING: This page is part of the old tutorials, please refer to the [[Tutorials|new documentation]]]'''<<BR>><<BR>><<BR>>
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- * A non-technical overview of MEG and EEG, with an emphasis on source modeling: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]],
+ * A non-technical overview of MEG and EEG, with an emphasis on source modeling:<<BR>> [[http://www.canada-meg-consortium.org/EN/MegIntro|Canada MEG Consortium]]
-Line 9:
+Line 11:
- * Slides from a selection of educational courses at [[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]],
+ * Slides from a selection of educational courses:<<BR>>[[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]]
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+Line 14:
-  * 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
+  * [[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]]<<BR>>Editors: P Hansen, M Kringelbach, R Salmelin, ''Oxford University Press'', 2010, 448 pages
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-  * 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]].
+  * [[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]]<<BR>>Editors: J Decety, JT Cacioppo, ''Oxford University Press'', 2011, 1128 pages<<BR>>A draft version of the MEG chapter by Sylvain Baillet can be found [[attachment:BailletMEGDraft.pdf|here]]. '' ''
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- * 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).
+ * [[http://www.ncbi.nlm.nih.gov/pubmed/23046981|Good practice for conducting and reporting MEG research]], Gross et al, Neuroimage, 2013

 * 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).
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-== 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.
+== Get started ==
The easiest way to get started with Brainstorm is to follow carefully these introduction tutorials. In  just a few hours, you will be introduced to the essential features of  the application. You will find a report form at the end of each tutorial, please share your comments to help us improve the documentation and the software. To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]].
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-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.
+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 these pages are updated with the software, and cannot be kept as long term reference documentation.
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-. [[Tutorials/BstFolders|Brainstorm architecture]]
 1. [[Tutorials/TutFirstSteps|First steps]]
 1. [[Tutorials/TutImportAnatomy|Importing individual anatomy]]
 1. [[Tutorials/TutImportRecordings|Importing MEG recordings]]
 1. [[Tutorials/TutExploreRecodings|Exploring the recordings]]
 1. [[Tutorials/TutHeadModel|Head model]]
 1. [[Tutorials/TutNoiseCov|Noise covariance]]
 1. [[Tutorials/TutSourceEstimation|Source estimation]]
 1. [[Tutorials/TutScouts|Scouts]]
 1. [[Tutorials/TutProcesses|Graphical scripting]]
 1. [[Tutorials/TutStat|Statistics]]
 1. [[Tutorials/TutTimefreq|Time-frequency]]
+=== 12 easy steps through Brainstorm ===
 1. [[Tutorials/BstFolders|Brainstorm architecture]]    ''[10 min] ''
 1. [[Tutorials/TutFirstSteps|First steps]]    ''[30 min]''
 1. [[Tutorials/TutImportAnatomy|Importing individual anatomy]]     ''[30 min]''
 1. [[Tutorials/TutImportRecordings|Importing MEG recordings]]     ''[30 min]''
 1. [[Tutorials/TutExploreRecodings|Exploring the recordings]]     ''[60 min]''
 1. [[Tutorials/TutHeadModel|Head model]]     ''[30 min]''
 1. [[Tutorials/TutNoiseCov|Noise covariance]]     ''[30 min]''
 1. [[Tutorials/TutSourceEstimation|Source estimation]]     ''[45 min]''
 1. [[Tutorials/TutScouts|Scouts]]     ''[45 min]''
 1. [[Tutorials/TutProcesses|Graphical scripting]]     ''[45 min]''
 1. [[Tutorials/TutStat|Statistics]]     ''[30 min]''
 1. [[Tutorials/TutTimefreq|Time-frequency]]     ''[1:30 hr'']

=== Processing continuous recordings ===
 1. [[Tutorials/TutRawViewer|Review continuous recordings and edit markers]] ''[2:00 hr]''
 1. [[Tutorials/TutRawSsp|Detect and remove artifacts]] ''[2:00 hr]''
 1. [[Tutorials/TutRawAvg|Epoching and averaging]] ''[1:30 hr]''
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-=== Processing continuous recordings ===
 1. [[Tutorials/TutRawViewer|Review continuous recordings and edit markers]] [2:00 hr]
 1. [[Tutorials/TutRawSsp|Detect and remove artifacts]] [2:00 hr]
 1. [[Tutorials/TutRawAvg|Epoching and averaging]] [1:30 hr]
+=== Complete analysis of other datasets ===
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG and epilepsy]]
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory|MEG auditory tutorial]]
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa|MEG median nerve (Yokogawa/KIT)]]
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag|MEG median nerve (Elekta-Neuromag)]]
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Resting|MEG resting state (CTF)]]
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-=== Other types of recordings ===
 1. EEG and Epilepsy
 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]]
+. [[http://neuroimage.usc.edu/brainstorm/Tutorials/RatPac|Rat electrophysiology]] [Under construction]
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-. [[Tutorials/LabelFreeSurfer|MRI segmentation: FreeSurfer]]
 1. [[Tutorials/SegBrainVisa|MRI segmentation: BrainVISA]]
+. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]]
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+. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]]
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-. [[Tutorials/TutRealtime|Realtime head positioning in the CTF MEG system]]
+. [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG system]]
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-. [[Tutorials/RefProcesses|Description of all the processes]]
+. [[SelectFiles|Selecting files in the database]]
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-. [[RefWriteProcess|How to write your own process]]
+. [[Tutorials/TutUserProcess|How to write your own process]]
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-. [[Tutorials/TutVolSource|Volumetric source estimation]]
+. [[Tutorials/TutVolSource|Volume source estimation]]
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-. [[Tutorials/TutXfit|Dipole models from Neuromag's Xfit and CTF's DipoleFit]]
+. [[Tutorials/TutDipScan|Computing and displaying dipoles]]

 1. [[Tutorials/Beamformers|Beamforming methods]] [Under construction]

 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction]

=== Functional connectivity ===
 1. [[Tutorials/TutPac|Phase-amplitude coupling]]

=== Statistics ===
 1. [[ExportSpm8|Export volume source maps to SPM8 / SPM12]]
 1. [[ExportSpm12|Export surface source maps to SPM12]]
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-. [[CoordinateSystems|Coordinate systems]]
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+. [[Tutorials/WorkflowGuide|MEG analysis guidelines for McGill]]

 1. [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]]

 1. [[Tutorials/ArtifactDetect|Detecting bad segments in continuous recordings]]

 1. [[Tutorials/MovementDetect|Detect subject movements]]

 1. [[Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]]

 1. [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm")

Software

Users

Development