= 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/Tutorials#Background_readings|background literature]].<
>To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]].<
><)>>If you are looking for the old tutorials, they are still available [[TutorialsOld|here]]. <)>> == Get started == The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. The number between brackets represents the number of printed pages for each tutorial. All in [[Tutorials/AllIntroduction|one page]]. <
>Some sections are still being edited or under review: [[Tutorials/Review|Editing process]]. <)>> '''Starting a new study''' <>1. [[Tutorials/CreateProtocol|Create a new protocol]] <)>>[9] <)>> <>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <)>>[8] <)>> <>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <)>>[13] <)>> '''Reviewing''' <>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <)>>[11] <)>> <>5. [[Tutorials/ReviewRaw|Continuous recordings]] <)>>[9] <)>> <>6. [[Tutorials/MultipleWindows|Multiple windows]] <)>>[5] <)>> <>7. [[Tutorials/EventMarkers|Event markers]] <)>>[10] <)>> '''Pre-processing''' <>8. [[Tutorials/StimDelays|Stimulation delays]] <)>>[9] <)>> <>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <)>>[11] <)>> <>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <)>>[15] <)>> <>11. [[Tutorials/BadChannels|Bad channels]] <)>>[6] <)>> <>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <)>>[8] <)>> <>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <)>>[16] <)>> <>14. [[Tutorials/BadSegments|Additional bad segments]] <)>>[7] <)>> <)>> '''Epoching and averaging''' <>15. [[Tutorials/Epoching|Import epochs]] <)>>[9] <)>> <>16. [[Tutorials/Averaging|Average response]] <)>>[7] <)>> <>17. [[Tutorials/ExploreRecordings|Visual exploration]] <)>>[10] <)>> <>18. [[Tutorials/Colormaps|Colormaps]] <)>>[5] <)>> <>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <)>>[4] <)>> '''Source modeling''' <>20. [[Tutorials/HeadModel|Head model]] <)>>[9] <)>> <>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <)>>[7] <)>> <>22. [[Tutorials/SourceEstimation|Source estimation]] <)>>[28] <)>> <>23. [[Tutorials/Scouts|Scouts]] <)>>[17] <)>> '''Advanced processing''' <>24. [[Tutorials/TimeFrequency|Time-frequency]] <)>>[33] <)>> <>25. [[Tutorials/Difference|Difference]] <)>>[13] <)>> <>26. [[Tutorials/Statistics|Statistics]] <)>>[30] <)>> <>27. [[Tutorials/Workflows|Workflows]] <)>>[10] <)>> <>28. [[Tutorials/Scripting|Scripting]] <)>>[31] <)>> <)>> == Other analysis scenarios == <)>> * [[Tutorials/Epilepsy|EEG and epilepsy]] * [[Tutorials/VisualSingle|MEG visual: single subject (Elekta)]] * [[Tutorials/VisualGroup|MEG visual: group study (Elekta)]] * [[Tutorials/PhantomCtf|MEG current phantom (CTF)]] * [[Tutorials/PhantomElekta|MEG current phantom (Elekta)]] * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] <)>> * [[Tutorials/TutMindNeuromag|MEG median nerve (Elekta)]] [TODO] * [[Tutorials/Yokogawa|MEG median nerve (Yokogawa)]] [TODO] * [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] [TODO] * [[Tutorials/Auditory|MEG auditory (CTF)]] [TODO] * [[Tutorials/Resting|MEG resting state / PAC (CTF)]] [TODO] <)>> == Advanced tutorials == <)>> '''Recordings''' * [[Tutorials/MontageEditor|Montage editor]] [TODO] * [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime|Real-time head-tracking]] * [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] <)>> '''Advanced processing''' * [[Tutorials/Connectivity|Functional connectivity]] [TODO] * [[Tutorials/TutPac|Phase-amplitude coupling]] * [[ExportSpm8|Export volume sources to SPM8/SPM12]] * [[ExportSpm12|Export surface sources to SPM12]] * [[Tutorials/Decoding|Decoding conditions (MVPA)]] * [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] * [[Tutorials/TutUserProcess|How to write your own process]] <)>> '''Anatomy and registration''' * [[CoordinateSystems|Brainstorm coordinate systems]] * [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] * [[Tutorials/DefaultAnatomy|Using the anatomy templates]] * [[Tutorials/TutWarping|Warping default anatomy]] * [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] * [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] * [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG]] <)>> '''Source modeling''' * [[Tutorials/TutBem|BEM with OpenMEEG]] * [[Tutorials/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] [TODO] * [[Tutorials/TutDipScan|Dipoles: Scanning and importing]] [TODO] * [[Tutorials/DipoleFitting|Dipoles: FieldTrip dipole fitting]] * [[Tutorials/Beamformers|Beamforming methods]] [TODO] * [[Tutorials/TutBEst|Maximum entropy on the mean (MEM)]] <)>> '''Other useful how-to's''' * [[CiteBrainstorm|How to cite Brainstorm]] * [[Tutorials/KnownBugs|Known bugs]] '''Tutorials from other authors''' * Video tutorial: [[http://www.jove.com/video/50212/how-to-detect-amygdala-activity-with-magnetoencephalography-using?status=a52218k|How to detect amygdala activity with MEG using source imaging]] * [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm") <)>> == 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: * [[http://www.canada-meg-consortium.org/EN/MegIntro|Canada MEG consortium: Basics of MEG]]<
>A non-technical overview of MEG and EEG, with an emphasis on source modeling. * [[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]]<
>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]]<
>Editors: J Decety, JT Cacioppo, ''Oxford University Press'', 2011, 1128 pages<
>A draft version of the MEG chapter by Sylvain Baillet can be found [[http://neuroimage.usc.edu/paperspdf/baillet_draft_2011.pdf|here]].'' '' * [[http://www.ncbi.nlm.nih.gov/pubmed/23046981|Good practice for conducting and reporting MEG research]], Gross et al, Neuroimage, 2013. * Slides from a selection of educational courses: [[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]] * We can also come and organize a [[Training|training session]] at your institution, or [[http://www.bic.mni.mcgill.ca/ResearchLabsNeuroSPEED/HomePage|visit us]] at the MNI. Now you are well equipped to go through the software tutorial, '' Enjoy! '' <
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