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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 [[http://neuroimage.usc.edu/brainstorm/TutorialsNew#Background_readings|background information]]. | 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 follow carefully those introduction tutorials. In just a few hours, you will be introduced to the essential features of the application. | 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]]. <<BR>>Some sections are still being edited or under review: [[Tutorials/Review|Editing process]]. |
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| 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''] |
<<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> |
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| '''Starting a new study''' | |
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| <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> | |
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| 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]'' |
<<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> '''Reviewing''' <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> '''Pre-processing''' <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[15] <<HTML(</FONT>)>> <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <<HTML(<FONT color="#DDDDDD">)>>[16] <<HTML(</FONT>)>> <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML(</TD><TD>)>> '''Epoching and averaging''' <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> '''Source modeling''' <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> '''[TODO]''' <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>>[17] <<HTML(</FONT>)>> '''Advanced processing''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[33] <<HTML(</FONT>)>> <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>>[30] <<HTML(</FONT>)>> <<HTML( )>>27. [[Tutorials/Workflows|Workflows]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>28. [[Tutorials/Scripting|Scripting]] <<HTML(<FONT color="#DDDDDD">)>>[31] <<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]] * [[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/BIDS)]] * [[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]''' <<HTML(</TD></TR></TABLE>)>> |
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| === Complete analysis of other datasets === 1. [[Tutorials/Epilepsy|EEG and epilepsy]] 1. [[Tutorials/Resting|Resting state MEG]] 1. [[Tutorials/Yokogawa|Yokogawa/KIT MEG recordings]] 1. [[Tutorials/TutMindNeuromag|Elekta-Neuromag recordings]] 1. [[Tutorials/Auditory|Brainstorm-FieldTrip auditory tutorial]] [Under construction] 1. [[Tutorials/RatPac|Rat electrophysiology]] [Under construction] |
<<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> |
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| === Anatomy and registration === 1. [[CoordinateSystems|Brainstorm coordinate systems]] 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegCIVET|CIVET]] |
'''Anatomy and registration''' |
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| 1. [[Tutorials/TutWarping|Warping default anatomy]] | * [[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 the anatomy templates]] * [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] * [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] * [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG]] |
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| 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] | '''Recordings''' |
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| 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] 1. [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG system]] |
* [[Tutorials/MontageEditor|Montage editor]] * [[Tutorials/SSPCookbook|SSP cookbook]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] * [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] |
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| === 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]] |
'''Software''' |
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| === Source modeling === 1. [[Tutorials/TutBem|BEM with OpenMEEG]] |
* [[CiteBrainstorm|How to cite Brainstorm]] [TODO] * [[Tutorials/KnownBugs|Known bugs]] * [[Tutorials/Plotly|Export figures to Plotly]] |
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| 1. [[Tutorials/TutVolSource|Volume source estimation]] | '''Deprecated documentation''' |
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| 1. [[Tutorials/TutDipScan|Computing and displaying dipoles]] | * [[Tutorials/VisualSingleOrig|MEG visual: single subject (Elekta/Orig)]] |
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| 1. [[Tutorials/Beamformers|Beamforming methods]] [Under construction] | * [[Tutorials/VisualGroupOrig|MEG visual: group study (Elekta/Orig)]] |
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| 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction] | <<HTML(</TD><TD>)>> |
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| === Functional connectivity === 1. [[Tutorials/TutPac|Phase-amplitude coupling]] |
'''Source modeling''' |
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| === Statistics === 1. [[ExportSpm8|Export volume source maps to SPM8 / SPM12]] 1. [[ExportSpm12|Export surface source maps to SPM12]] |
* [[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]] |
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| === Other useful how-to's === 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] |
'''Advanced processing''' |
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| 1. [[Tutorials/KnownBugs|Known bugs]] | * [[Tutorials/TutUserProcess|How to write your own process]] * [[Tutorials/Decoding|Decoding conditions (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/MicrostatesCena|Microstate segmentation with CENA]] * [[ExportSpm8|Export volume sources to SPM8/SPM12]] * [[ExportSpm12|Export surface sources to SPM12]] |
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| 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(</TD></TR></TABLE>)>> |
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| * 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]] | * [[http://www.canada-meg-consortium.org/EN/MegIntro|Canada MEG consortium: Basics of MEG]]<<BR>>A non-technical overview of MEG and EEG, with an emphasis on source modeling. |
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| * Slides from a selection of educational courses:<<BR>>[[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]] | * [[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. |
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| * 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 [[http://neuroimage.usc.edu/paperspdf/baillet_draft_2011.pdf|here]].'' '' |
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| * [[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. |
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| * [[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]] |
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| * 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). | * 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. |
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<<BR>><<BR>><<BR>><<BR>><<BR>> |
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. The number between brackets represents the number of printed pages for each tutorial. All in one page.
Some sections are still being edited or under review: Editing process.
| Starting a new study 1. Create a new protocol [9] 2. Import the subject anatomy [8] 3. Explore the anatomy [13] Reviewing 4. Channel file / MRI registration [11] 5. Continuous recordings [9] 6. Multiple windows [5] 7. Event markers [10] Pre-processing 8. Stimulation delays [9] 9. Select files / Run processes [11] 10. Power spectrum / Frequency filters [15] 11. Bad channels [6] 12. Artifact detection [8] 13. Artifact cleaning with SSP [16] 14. Additional bad segments [7] | Epoching and averaging 15. Import epochs [9] 16. Average response [7] 17. Visual exploration [10] 18. Colormaps [5] 19. Clusters of sensors [4] Source modeling 20. Head model [9] 21. Noise/data covariance [7] 22. Source estimation [28] [TODO] 23. Scouts [17] Advanced processing 24. Time-frequency [33] 25. Difference [13] 26. Statistics [30] 27. Workflows [10] 28. Scripting [31] |
Other analysis scenarios
Advanced tutorials
| Anatomy and registration Recordings Software Deprecated documentation | Source modeling Advanced processing |
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:
Canada MEG consortium: Basics of MEG
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!