= 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]].
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'''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] <)>> '''[TODO]'''
<>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] <)>>
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== Other analysis scenarios ==
<)>>
* [[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)]]
< | )>>
* [[Tutorials/RestingOmega|MEG resting state & OMEGA database (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]] ''' [TODO]'''
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== Advanced tutorials ==
<)>>
'''Anatomy and registration'''
* [[CoordinateSystems|Brainstorm coordinate systems]]
* MRI segmentation:[[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], < >[[Tutorials/SegBrainVisa|BrainVISA]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT12]], [[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]]
* [[Tutorials/SSPCookbook|SSP cookbook]]
* [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]]
* [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]]
'''Software'''
* [[CiteBrainstorm|How to cite Brainstorm]] [TODO]
* [[Tutorials/KnownBugs|Known bugs]]
* [[Tutorials/Plotly|Export figures to Plotly]]
'''Deprecated documentation'''
* [[Tutorials/VisualSingleOrig|MEG visual: single subject (Elekta/Orig)]]
* [[Tutorials/VisualGroupOrig|MEG visual: group study (Elekta/Orig)]]
< | )>>
'''Source modeling'''
* [[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]]
* [[Tutorials/TutVolSource|Volume source estimation]]
* [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]]
* [[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]]
'''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/Connectivity|Functional connectivity]] [TODO]
* [[Tutorials/FiberConnectivity|Virtual fibers for connectivity]]
* [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]]
'''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]]
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== Invasive neurophysiology ==
Learn how to use Brainstorm for studying single & multiunit activity.
<)>>
* [[https://neuroimage.usc.edu/brainstorm/e-phys/Introduction|Importing raw e-phys data]]
* [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting#Supervised_Spike_Sorting|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]]
< | )>>
* [[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]]
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== 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:
* [[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)]] <
>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/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.
Now you are well equipped to go through the software tutorial, '' Enjoy! ''
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