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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. The number between brackets represents the number of printed pages for each tutorial. | 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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| <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> | <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> |
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| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> | <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> | <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
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| <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> | <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[15] <<HTML(</FONT>)>> |
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| <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> | <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
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| <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> | <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> | <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
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| <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> | <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> | <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
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| <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[26] <<HTML(</FONT>)>> | <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> |
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| '''Advanced signal processing''' | '''Advanced processing''' |
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| <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[22] <<HTML(</FONT>)>> | <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[33] <<HTML(</FONT>)>> |
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| <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] [Under construction] | <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> |
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| <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] [Under construction] | <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>>[30] <<HTML(</FONT>)>> |
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| <<HTML( )>>27. [[Tutorials/Scripting|Complete tutorial script]] [Under construction] | <<HTML( )>>27. [[Tutorials/Workflows|Workflows]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>28. [[Tutorials/Scripting|Scripting]] <<HTML(<FONT color="#DDDDDD">)>>[31] <<HTML(</FONT>)>> |
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| 1. [[Tutorials/Epilepsy|EEG and epilepsy]] 1. [[Tutorials/Auditory|MEG auditory tutorial (CTF)]] 1. [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] [Under construction] 1. [[Tutorials/Yokogawa|MEG median nerve (Yokogawa/KIT)]] 1. [[Tutorials/TutMindNeuromag|MEG median nerve (Elekta-Neuromag)]] [Under construction] 1. [[Tutorials/Resting|MEG resting state (CTF)]] 1. [[Tutorials/VisualSingle|MEG visual single subject (Elekta-Neuromag)]] [Under construction] 1. [[Tutorials/VisualGroup|MEG visual group study (Elekta-Neuromag)]] [Under construction] |
<<HTML(<TABLE class="tuto-table"><TR><TD>)>> * [[Tutorials/Epilepsy|EEG and epilepsy]] [TODO] * [[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]] <<HTML(</TD><TD>)>> * [[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] <<HTML(</TD></TR></TABLE>)>> |
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| === Recordings === 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] 1. ICA decomposition [Under construction] 1. [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] |
<<HTML(<TABLE class="tuto-table"><TR><TD>)>> |
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| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]] | '''Recordings''' |
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| === 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] |
* [[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]] |
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| 1. [[Tutorials/TutWarping|Warping default anatomy]] | <<HTML(</TD><TD>)>> |
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| 1. [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] | '''Advanced processing''' |
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| 1. Group analysis: Averaging [Under construction] | * [[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]] |
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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]] |
<<HTML(</TD></TR><TR><TD>)>> |
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| === Source modeling === 1. [[Tutorials/TutBem|BEM with OpenMEEG]] |
'''Anatomy and registration''' |
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| 1. [[Tutorials/TutVolSource|Volume source estimation]] | * [[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]] |
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| 1. [[Tutorials/TutDipScan|Computing and displaying dipoles]] | <<HTML(</TD><TD>)>> |
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| 1. [[Tutorials/Beamformers|Beamforming methods]] [Under construction] | '''Source modeling''' |
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| 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction] | * [[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)]] * [[Tutorials/EpilepsyBest|MEM Epilepsy]] [TODO] |
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| === Advanced processing === 1. [[Tutorials/TutPac|Phase-amplitude coupling]] |
<<HTML(</TD></TR></TABLE>)>> |
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| 1. [[ExportSpm8|Export volume source maps to SPM8 / SPM12]] 1. [[ExportSpm12|Export surface source maps to SPM12]] 1. [[Tutorials/Decoding|Decoding conditions (MVPA)]] 1. [[Tutorials/TutUserProcess|How to write your own process]] |
'''Other useful how-to's''' |
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| === Other useful how-to's === 1. [[Tutorials/IPythonNotebook|Brainstorm on IPython Notebook]] 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] |
* [[CiteBrainstorm|How to cite Brainstorm]] * [[Tutorials/KnownBugs|Known bugs]] |
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| 1. [[Tutorials/KnownBugs|Known bugs]] | '''Tutorials from other authors''' |
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| 1. [[Tutorials/AllIntroduction|All the introduction tutorials on the same page]] | * 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]] |
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| === Tutorials from other authors === 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 1. [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm") 1. [[Tutorials/WorkflowGuide|MEG analysis guidelines for McGill]] |
* [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm") |
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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 [[attachment:BailletMEGDraft.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] 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
| Recordings | Advanced processing |
| Anatomy and registration | Source modeling
|
Other useful how-to's
Tutorials from other authors
Video tutorial: How to detect amygdala activity with MEG using source imaging
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:
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!