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| <<HTML(<TABLE class="tuto-table"><TR><TD>)>> | <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> |
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| <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> | <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> [TODO] |
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| <<HTML(<TABLE class="tuto-table"><TR><TD>)>> | <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> |
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| * [[Tutorials/Epilepsy|EEG and epilepsy]] [TODO] | * [[Tutorials/Epilepsy|EEG and epilepsy]] |
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| * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] | |
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| * [[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] |
* [[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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| <<HTML(<TABLE class="tuto-table"><TR><TD>)>> | <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> '''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 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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| * [[Tutorials/MontageEditor|Montage editor]] [TODO] * [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]] |
* [[Tutorials/MontageEditor|Montage editor]] * [[Tutorials/SSPCookbook|SSP cookbook]] |
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| * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]] | |
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| <<HTML(</TD><TD>)>> | '''Software''' |
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| '''Advanced processing''' * [[Tutorials/Connectivity|Functional connectivity]] [TODO] * [[Tutorials/TutPac|Phase-amplitude coupling]] * [[ExportSpm8|Export volume source maps to SPM8 / SPM12]] * [[ExportSpm12|Export surface source maps to SPM12]] * [[Tutorials/Decoding|Decoding conditions (MVPA)]] * [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] * [[Tutorials/TutUserProcess|How to write your own process]] <<HTML(</TD></TR><TR><TD>)>> '''Anatomy and registration''' * [[CoordinateSystems|Brainstorm coordinate systems]] * MRI segmentation: [[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 system]] |
* [[CiteBrainstorm|How to cite Brainstorm]] [TODO] * [[Tutorials/KnownBugs|Known bugs]] |
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| * [[Tutorials/TutBem|BEM with OpenMEEG]] | * [[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]] |
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| * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] [Under construction] * [[Tutorials/TutDipScan|Computing and displaying dipoles]] [Must be updated] * [[Tutorials/DipoleFitting|Dipole fitting with FieldTrip]] * [[Tutorials/Beamformers|Beamforming methods]] [Under construction] * [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] * [[Tutorials/EpilepsyBest|MEM Epilepsy]] [TODO] |
* [[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/TutBEst|Maximum entropy on the mean (MEM)]] * [[Tutorials/Beamformers|Beamforming methods]] [TODO] |
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| <<HTML(</TD></TR><TR><TD>)>> | '''Advanced processing''' |
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| '''Other useful how-to's''' * [[CiteBrainstorm|How to cite Brainstorm in your publications]] * [[Tutorials/KnownBugs|Known bugs]] <<HTML(</TD><TD>)>> '''Tutorials from other authors''' 1. 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]] 1. [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm") |
* [[Tutorials/TutUserProcess|How to write your own process]] * [[Tutorials/Decoding|Decoding conditions (MVPA)]] * [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] * [[Tutorials/TutPac|Phase-amplitude coupling: Method]] [TODO] * [[Tutorials/Resting|Phase-amplitude coupling: Example]] [TODO] * [[Tutorials/Connectivity|Functional connectivity]] [TODO] * [[ExportSpm8|Export volume sources to SPM8/SPM12]] * [[ExportSpm12|Export surface sources to SPM12]] |
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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. |
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
| 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!