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| '''[UNDER CONSTRUCTION]''' 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]].<<BR>>To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]]. |
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. | 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( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] | <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] | <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
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| <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] | <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> |
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| <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] | <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
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| <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] | <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] | <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
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| <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] | <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] | <<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( )>>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( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[15] <<HTML(</FONT>)>> |
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| <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] [Under construction] | <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> |
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| <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] | <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
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| <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] [Under construction] | <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <<HTML(<FONT color="#DDDDDD">)>>[16] <<HTML(</FONT>)>> |
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| <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] [Under construction] '''Epoching and averaging''''''<<BR>>[Under construction] ''' <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] [Under construction] <<HTML( )>>16. [[Tutorials/Averaging|Average response]] [Under construction] <<HTML( )>>17. [[Tutorials/ExploreRecordings|Exploring the average response]] <<HTML( )>>18. 2D/3D topography <<HTML( )>>19. [[Tutorials/Colormaps|Colormaps]] |
<<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
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| '''Source modeling''''''<<BR>>[Under construction] ''' | '''Epoching and averaging''' |
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| <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] | <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise covariance]] | <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
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| <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] | <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] | <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
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| '''Advanced signal processing''''''<<BR>>[Under construction] ''' | <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> |
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| <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] | '''Source modeling''' |
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| <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] | <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] | <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
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| <<HTML( )>>27. Phase-amplitude coupling | <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> |
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| '''Scripting'''''' <<BR>>[Under construction] ''' | <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>>[17] <<HTML(</FONT>)>> |
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| <<HTML( )>>28. [[Tutorials/Scripting|Complete tutorial script]] | '''Advanced processing''' |
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| <<HTML( )>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]] | <<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>)>> |
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| == 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]] |
== Other analysis scenarios == <<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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| === Interface === 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] 1. ICA decomposition [Under construction] |
<<HTML(<TABLE class="tuto-table"><TR><TD>)>> |
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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] |
'''Recordings''' |
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| 1. [[Tutorials/TutWarping|Warping default anatomy]] | * [[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/CoregisterSubjects|Group analysis: Subjects coregistration]] | <<HTML(</TD><TD>)>> |
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| 1. Group analysis: Averaging [Under construction] | '''Advanced processing''' |
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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/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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| === Scripting === 1. [[Tutorials/TutUserProcess|How to write your own process]] |
<<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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| === Functional connectivity === 1. [[Tutorials/TutPac|Phase-amplitude coupling]] |
<<HTML(</TD></TR></TABLE>)>> |
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| === Statistics === 1. [[ExportSpm8|Export volume source maps to SPM8 / SPM12]] 1. [[ExportSpm12|Export surface source maps to SPM12]] |
'''Other useful how-to's''' |
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| === Other useful how-to's === 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/WorkflowGuide|MEG analysis guidelines for McGill]] | * 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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| 1. [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]] 1. [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm") === 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 |
* [[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!