= 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.

== 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:<<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! ''

== Get started ==
The easiest way to get started with Brainstorm is to follow carefully those 12+3 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.

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.

=== 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]''

== Advanced tutorials ==
=== Complete analysis of other datasets ===
 1. [[Tutorials/Epilepsy|EEG and epilepsy]]
 1. [[Tutorials/Yokogawa|Yokogawa/KIT recordings]]
 1. [[Tutorials/TutMindNeuromag|Elekta-Neuromag recordings]] [Not up to date]
 1. [[Tutorials/Resting|Resting state MEG]] [Under construction]
 1. [[Tutorials/RatPac|Rat electrophysiology]] [Under construction]
 1. [[Tutorials/Auditory|Brainstorm-FieldTrip auditory tutorial]] [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/TutWarping|Warping default anatomy]]

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

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

=== Graphical 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]

=== Functional connectivity ===
 1. [[Tutorials/TutPac|Phase-amplitude coupling]]
 1. Cortico-muscular coherence  [Under construction]

=== 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