= 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 [[http://neuroimage.usc.edu/brainstorm/TutorialsNew#Background_readings|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.

<<HTML(<TABLE class="tuto-table"><TR><TD>)>>

==== Starting a new study ====
<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>1. [[Tutorials/CreateProtocol|Create a new protocol]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]]

'''Reviewing and pre-processing'''

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>4. [[Tutorials/ChannelFile|Channel file & MRI coregistration]]

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

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>6. [[Tutorials/MultipleWindows|Multiple windows]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>7. [[Tutorials/EventMarkers|Event markers]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>8. [[Tutorials/StimDelays|Stimulation delays]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>9. [[Tutorials/ArtifactsFilter|Frequency filters]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>10. [[Tutorials/BadChannels|Bad channels]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>11. [[Tutorials/ArtifactsDetect|Artifact detection]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>12.  [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]]  [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>13.  [[Tutorials/BadSegments|Additional bad segments]]  [Under construction]

'''Epoching and averaging''' [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>14. [[Tutorials/Epoching|Import epochs]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>15. [[Tutorials/Averaging|Average response]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>16. [[Tutorials/ExploreRecordings|Exploring the average response]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>17. 2D/3D topography

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>18. [[Tutorials/Colormaps|Colormaps]]

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'''Source modeling''' [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>19. [[Tutorials/HeadModel|Head model]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>20. [[Tutorials/NoiseCovariance|Noise covariance]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>21. [[Tutorials/SourceEstimation|Source estimation]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>22. [[Tutorials/Scouts|Scouts]]

'''Advanced topics''' [Under construction]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>23. [[Tutorials/TimeFrequency|Time-frequency]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>24. [[Tutorials/Statistics|Statistics]]

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

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>26. Phase-amplitude coupling

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>27. [[Tutorials/Scripting|Advanced scripting]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>28. Complete tutorial script

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>29. Summary

<<HTML(</TD></TR></TABLE>)>>

== 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. [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]]   [Under construction]
 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)]]     [Under construction]
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Resting|MEG resting state]]

== Advanced tutorials ==
=== Interface ===
 1. [[Tutorials/MontageEditor|Montage editor]]   [Under construction]

=== Anatomy and registration ===
 1. [[CoordinateSystems|Brainstorm coordinate systems]]
 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegCIVET|CIVET]]
 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]]  [Under construction]

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

 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]]

 1. Group studies: Averaging

 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]]
 1. [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG system]]

=== Scripting ===
 1. [[SelectFiles|Selecting files in the database]]
 1. [[Tutorials/TutRawScript|Full analysis with one script]]
 1. [[Tutorials/TutUserProcess|How to write your own process]]

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

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

 1. [[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]]

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

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

 1. [[Tutorials/WorkflowGuide|MEG analysis guidelines for McGill]]

=== Examples ===
 1. This video illustrates how Brainstorm can be used for studying amygdala activity:<<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]] <<BR>>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:<<BR>> [[http://www.canada-meg-consortium.org/EN/MegIntro|Canada MEG Consortium]]

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

 * Reference books:
  * [[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

  * [[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]]. '' ''

 * [[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).

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

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