= Tutorials =
'''[UNDER CONSTRUCTION]'''

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]].<<BR>>To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]].

== 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(</FONT color="#CCCCCC">)>>[9] <<HTML(</FONT>)>>

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(</FONT color="#CCCCCC">)>>[8] <<HTML(</FONT>)>>

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

'''Reviewing'''

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

<<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]]

'''Pre-processing'''

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

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>9. [[Tutorials/PipelineEditor|Select files / Run processes]]

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

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

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

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

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>14.  [[Tutorials/BadSegments|Additional bad segments]]

'''Epoching and averaging''''''<<BR>>[Under construction]  '''

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>15. [[Tutorials/Epoching|Import epochs]]

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

<<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]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>?? Clusters of sensors

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'''Source modeling''''''<<BR>>[Under construction]  '''

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>20. [[Tutorials/HeadModel|Head model]]

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

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>22. [[Tutorials/SourceEstimation|Source estimation]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>23. [[Tutorials/Scouts|Scouts]]

'''Advanced signal processing''''''<<BR>>[Under construction]  '''

<<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

'''Scripting''''''  <<BR>>[Under construction] '''

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>28. [[Tutorials/Scripting|Complete tutorial script]]

<<HTML(&nbsp;&nbsp;&nbsp;&nbsp;)>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]]

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

== Other analysis scenarios ==
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG and epilepsy]]
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory|MEG auditory tutorial (CTF)]]
 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 (CTF)]]

== Advanced tutorials ==
=== Recordings ===
 1. [[Tutorials/MontageEditor|Montage editor]]   [Under construction]
 1. ICA decomposition [Under construction]
 1. [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]]
 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]]

 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]]

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

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

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

 1. Group analysis: Averaging   [Under construction]

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

=== 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]

=== Advanced processing ===
 1. [[Tutorials/TutPac|Phase-amplitude coupling]]

 1. [[ExportSpm8|Export volume source maps to SPM8 / SPM12]]
 1. [[ExportSpm12|Export surface source maps to SPM12]]
 1. [[Tutorials/TutUserProcess|How to write your own process]]

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

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

=== Tutorials from other authors ===
 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
 1. [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm")
 1. [[Tutorials/WorkflowGuide|MEG analysis guidelines for McGill]]

== 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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