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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]]. | '''[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]]. |
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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. In just a few hours, you will be introduced to the essential features of the application. |
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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>)>> |
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| '''Starting a new study''' | |
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| <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] | |
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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( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] '''Reviewing''' <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file & MRI coregistration]] <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] '''Pre-processing''' <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files and run processes]] <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Frequency filters]] <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] [Under construction] <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] [Under construction] <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] [Under construction] <<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(</TD><TD>)>> '''Source modeling''''''<<BR>>[Under construction] ''' <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise covariance]] <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] '''Advanced signal processing''''''<<BR>>[Under construction] ''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] <<HTML( )>>27. Phase-amplitude coupling '''Scripting'''''' <<BR>>[Under construction] ''' <<HTML( )>>28. [[Tutorials/Scripting|Complete tutorial script]] <<HTML( )>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]] <<HTML(</TD></TR></TABLE>)>> == 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]] |
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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] |
=== Interface === 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] |
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| 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegCIVET|CIVET]] | 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] [Under construction] |
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| 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] | 1. [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] 1. Group analysis: Averaging [Under construction] |
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| === Graphical scripting === 1. [[SelectFiles|Selecting files in the database]] 1. [[Tutorials/TutRawScript|Full analysis with one script]] |
=== Scripting === |
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| 1. [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]] 1. [[Tutorials/ArtifactDetect|Detecting bad segments in continuous recordings]] 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") |
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<<BR>><<BR>><<BR>><<BR>><<BR>> |
Tutorials
[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 background literature.
To get a quick overview of the software interface, you can watch this introduction video.
Get started
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.
| Starting a new study Reviewing 4. Channel file & MRI coregistration Pre-processing 9. Select files and run processes 11. Bad channels [Under construction] 12. Artifact detection [Under construction] 13. Artifact cleaning with SSP [Under construction] 14. Additional bad segments [Under construction] Epoching and averaging 15. Import epochs [Under construction] 16. Average response [Under construction] 17. Exploring the average response 18. 2D/3D topography 19. Colormaps | Source modeling 20. Head model 21. Noise covariance 23. Scouts Advanced signal processing 24. Time-frequency 25. Statistics 26. Connectivity 27. Phase-amplitude coupling Scripting |
Complete analysis of other datasets
MEG median nerve (CTF) [Under construction]
MEG median nerve (Elekta-Neuromag) [Under construction]
Advanced tutorials
Interface
Montage editor [Under construction]
Anatomy and registration
MRI segmentation: FreeSurfer, BrainSuite, BrainVISA, CIVET
Using the anatomy templates [Under construction]
- Group analysis: Averaging [Under construction]
Scripting
Source modeling
Beamforming methods [Under construction]
Maximum Entropy on the Mean (MEM) [Under construction]
Functional connectivity
Statistics
Other useful how-to's
?MEG analysis guidelines for McGill
?Detecting bad segments in continuous recordings
A tutorial in Japanese (click on the menu "Brainstorm")
Examples
This video illustrates how Brainstorm can be used for studying amygdala activity:
How to Detect Amygdala Activity with Magnetoencephalography using Source Imaging
Authors: Balderston NL, Schultz DH, Baillet S, Helmstetter FJ
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:
A non-technical overview of MEG and EEG, with an emphasis on source modeling:
Canada MEG ConsortiumSlides from a selection of educational courses:
megcommunity.org- Reference books:
MEG: An Introduction to Methods
Editors: P Hansen, M Kringelbach, R Salmelin, Oxford University Press, 2010, 448 pagesThe 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
You can also ask us to come and organize a training session at your institution, or visit us to obtain training (McGill's Montreal Neurological Institute).
Now you are well equipped to go through the software tutorial, Enjoy!