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| 1. [[Tutorials/CreateProtocol|Create a new protocol]] 1. [[Tutorials/ImportAnatomy|Import the subject anatomy]] 1. [[Tutorials/ExploreAnatomy|Explore the anatomy]] 1. [[ChannelFile|Coregistration MEG-MRI]] [Under construction] 1. [[Tutorials/ReviewRaw|Review continuous files]] [Under construction] 1. [[MontageEditor|Montage editor]] [Under construction] 1. [[Tutorials/EventMarkers|Edit event markers]] [Under construction] 1. Artifacts: Frequency filters [Under construction] 1. Artifacts: Cleaning with SSP [Under construction] 1. Epoching 1. Averaging |
<<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]] <<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''' <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] [Under construction] <<HTML( )>>16. [[Tutorials/Averaging|Average response]] [Under construction] <<HTML( )>>17. [[Tutorials/ExploreRecordings|Exploring the average response]] [Under construction] <<HTML( )>>18. 2D/3D topography [Under construction] <<HTML( )>>19. [[Tutorials/Colormaps|Colormaps]] [Under construction] <<HTML(</TD><TD>)>> '''Source modeling''' <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] [Under construction] <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise covariance]] [Under construction] <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] [Under construction] <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] [Under construction] '''Advanced signal processing''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] [Under construction] <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] [Under construction] <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] [Under construction] <<HTML( )>>27. Phase-amplitude coupling [Under construction] '''Scripting''' <<HTML( )>>28. [[Tutorials/Scripting|Complete tutorial script]] [Under construction] <<HTML( )>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]] [Under construction] <<HTML(</TD></TR></TABLE>)>> |
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| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory|MEG auditory tutorial (CTF)]] | 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory|MEG auditory tutorial]] 1. [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] [Under construction] |
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| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag|MEG median nerve (Elekta-Neuromag)]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Resting|MEG resting state (CTF)]] |
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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| === 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. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] |
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 === |
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.
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 [Under construction] 18. 2D/3D topography [Under construction] 19. Colormaps [Under construction] | Source modeling 20. Head model [Under construction] 21. Noise covariance [Under construction] 22. Source estimation [Under construction] 23. Scouts [Under construction] Advanced signal processing 24. Time-frequency [Under construction] 25. Statistics [Under construction] 26. Connectivity [Under construction] 27. Phase-amplitude coupling [Under construction] Scripting 28. Complete tutorial script [Under construction] 29. All the tutorials on the same page [Under construction] |
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
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!