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| 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]]. | 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]].<<BR>>To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]].<<BR>><<HTML(<FONT color="#C0C0C0" >)>>If you are looking for the old tutorials, they are still available [[TutorialsOld|here]]. <<HTML(</FONT>)>> |
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| 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>)>> |
The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. They can be separately consulted (links below), or all in [[Tutorials/AllIntroduction|one page]]. <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> |
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| <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] |
<<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> |
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| <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file & MRI coregistration]] <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] |
<<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> |
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| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files and run processes]] <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Frequency filters]] <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] [Under construction] <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] [Under construction] <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] [Under construction] <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] [Under construction] |
<<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML(</TD><TD>)>> |
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| <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] [Under construction] <<HTML( )>>16. [[Tutorials/Averaging|Average response]] [Under construction] <<HTML( )>>17. [[Tutorials/ExploreRecordings|Exploring the average response]] [Under construction] <<HTML( )>>18. 2D/3D topography <<HTML( )>>19. [[Tutorials/Colormaps|Colormaps]] <<HTML(</TD><TD>)>> '''Source modeling ''' [Under construction] <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise covariance]] <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] '''Advanced signal processing ''' [Under construction] <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] <<HTML( )>>27. Phase-amplitude coupling '''Scripting ''' [Under construction] <<HTML( )>>28. [[Tutorials/Scripting|Complete tutorial script]] <<HTML( )>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]] <<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]] |
<<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> '''Source modeling''' <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> '''Advanced processing''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>27. [[Tutorials/Workflows|Workflows]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>28. [[Tutorials/Scripting|Scripting]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML(</TD></TR></TABLE>)>> == Other analysis scenarios == <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> * [[Tutorials/Epilepsy|EEG and epilepsy]] * [[Tutorials/Epileptogenicity|SEEG epileptogenicity maps]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG|ECoG+sEEG epilepsy (BIDS)]] * [[Tutorials/VisualSingle|MEG visual: single subject (Elekta/BIDS)]] * [[Tutorials/VisualGroup|MEG visual: group study (Elekta/BIDS)]] * [[Tutorials/PhantomCtf|MEG current phantom (CTF)]] * [[Tutorials/PhantomElekta|MEG current phantom (Elekta)]] <<HTML(</TD><TD>)>> * [[Tutorials/RestingOmega|MEG resting state & OMEGA database (CTF)]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence|MEG corticomuscular coherence (CTF)]] * [[Tutorials/HCP-MEG|MEG Human Connectome Project (4D)]] * [[Tutorials/TutMindNeuromag|MEG median nerve (Elekta)]] * [[Tutorials/Yokogawa|MEG median nerve (Yokogawa)]] * [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] <<HTML(</TD></TR></TABLE>)>> |
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| === Interface === 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] === 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]] === Scripting === 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 |
<<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> '''Anatomy and registration''' * [[CoordinateSystems|Brainstorm coordinate systems]] * MRI segmentation: [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT12]], [[Tutorials/LabelFreeSurfer|FreeSurfer]], <<BR>>[[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegFastSurfer|FastSurfer]], [[Tutorials/SegCIVET|CIVET]] * [[Tutorials/DefaultAnatomy|Using the anatomy templates]] * [[Tutorials/TutWarping|Warping the anatomy templates]] * [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] * [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] * [[Tutorials/TutRealtime|Real-time head positioning (CTF MEG)]] * [[Tutorials/HeadMotion|Head motion detection (MEG)]] '''Recordings''' * [[Tutorials/MontageEditor|Montage editor]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Artifact_cleaning_with_ICA|ICA analysis]] * [[Tutorials/SSPCookbook|SSP cookbook]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] * [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] '''Scripting''' * [[Tutorials/TutUserProcess|How to write your own process]] * [[ExportSpm8|Export volume sources to SPM8/SPM12]] * [[ExportSpm12|Export surface sources to SPM12]] * [[ExportBids|Export raw data to BIDS format]] '''Software''' * [[Tutorials/Plugins|Plugins]] * [[MnePython|MNE-Python]] * [[CiteBrainstorm|How to cite Brainstorm]] * [[Tutorials/KnownBugs|Known bugs]] * [[Tutorials/Plotly|Export figures to Plotly]] <<HTML(</TD><TD>)>> '''Source modeling''' * [[Tutorials/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] * [[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]] * [[Tutorials/TutDipScan|Dipoles: Scanning and displaying]] * [[Tutorials/DipoleFitting|Dipoles: FieldTrip dipole fitting]] * [[Tutorials/TutBEst|Maximum entropy on the mean (MEM)]] * [[Tutorials/Beamformers|Other beamforming methods]] * [[Tutorials/Simulations|Simulations]] '''Finite Element Modeling''' * [[Tutorials/Duneuro|Realistic head model: FEM with DUNEuro]] * [[Tutorials/FemMesh|FEM mesh generation]] * [[Tutorials/FemTensors|FEM tensors estimation]] * [[Tutorials/FemMedianNerve|FEM median nerve example]] '''Signal processing''' * [[Tutorials/Decoding|Machine learning: Decoding / MVPA]] * [[Tutorials/TutPac|Phase-amplitude coupling: Method]] * [[Tutorials/Resting|Phase-amplitude coupling: Example]] * [[Tutorials/PLS|Partial Least Squares (PLS)]] * [[Tutorials/EZFingerprint|Epileptogenic Zone Fingerprint]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof|FOOOF: Fitting Oscillations & One-Over-F]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT|SPRiNT: Spectral Param. Resolved in Time]] '''Connectivity''' * [[Tutorials/Connectivity|Functional connectivity]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence|Corticomuscular coherence]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph|Connectivity graphs]] * [[Tutorials/FiberConnectivity|Virtual fibers for connectivity]] * [[https://neuroimage.usc.edu/brainstorm/GrangerCausality|Granger causality]] <<HTML(</TD></TR></TABLE>)>> == Multiunit electrophysiology == Learn how to use Brainstorm for studying single & multiunit activity. <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> * [[https://neuroimage.usc.edu/brainstorm/e-phys/Introduction|Importing raw e-phys data]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting|Spike-sorting]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents|Using external spike-sorters]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP|Converting raw data to LFP]] <<HTML(</TD><TD>)>> * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions|Tuning curves]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Noise_correlation|Noise correlation]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Spike_field_coherence|Spike field coherence]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Raster_plots|Raster plots]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Spike_triggered_average|Spike triggered average]] <<HTML(</TD></TR></TABLE>)>> |
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| 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). |
These tutorial pages suppose you are comfortable with the basic concepts of MEG and EEG source imaging. If you're not, we encourage you to read some background information, which will quickly help you getting up to speed with this field: * [[http://rdcu.be/pydB|Nature Neuroscience review paper on MEG for Human Electrophysiology and Imaging]] (Baillet S, 2017) * [[https://www.mcw.edu/Magnetoencephalography-Program-MEG/About-MEG.htm|Introduction to MEG (Medical College of Wisconsin)]] <<BR>>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]]<<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 [[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/education/teaching-slides|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. |
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 background literature.
To get a quick overview of the software interface, you can watch this introduction video.
If you are looking for the old tutorials, they are still available ?here.
Get started
The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. They can be separately consulted (links below), or all in one page.
| Starting a new study Reviewing 4. Channel file / MRI registration Pre-processing 9. Select files / Run processes 10. Power spectrum / Frequency filters 11. Bad channels | Epoching and averaging 15. Import epochs 16. Average response 18. Colormaps Source modeling 20. Head model 23. Scouts Advanced processing 24. Time-frequency 25. Difference 26. Statistics 27. Workflows 28. Scripting |
Other analysis scenarios
Advanced tutorials
| Anatomy and registration
Recordings Scripting Software | Source modeling Finite Element Modeling Signal processing Connectivity |
Multiunit electrophysiology
Learn how to use Brainstorm for studying single & multiunit activity.
Background readings
These tutorial pages suppose you are comfortable with the basic concepts of MEG and EEG source imaging. If you're not, we encourage you to read some background information, which will quickly help you getting up to speed with this field:
Nature Neuroscience review paper on MEG for Human Electrophysiology and Imaging (Baillet S, 2017)
Introduction to MEG (Medical College of Wisconsin)
A non-technical overview of MEG and EEG, with an emphasis on source modeling.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.
Slides from a selection of educational courses: megcommunity.org
We can also come and organize a training session at your institution, or visit us at the MNI.
Now you are well equipped to go through the software tutorial, Enjoy!