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| 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]]. | 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 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. 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. |
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| ==== Starting a new study ==== <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] |
'''Starting a new study''' |
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| <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] | <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] | <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
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| ==== Reviewing and pre-processing ==== <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file & MRI coregistration]] |
<<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] | '''Reviewing''' |
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| <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] | <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
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| <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] | <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] [Under construction] | <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
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| <<HTML( )>>9. [[Tutorials/ArtifactsFilter|Frequency filters]] [Under construction] | <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>10. [[Tutorials/BadChannels|Bad channels]] [Under construction] | '''Pre-processing''' |
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| <<HTML( )>>11. [[Tutorials/ArtifactsDetect|Artifact detection]] [Under construction] | <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>12. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] [Under construction] | <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>13. [[Tutorials/BadSegments|Additional bad segments]] [Under construction] | <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <<HTML(<FONT color="#DDDDDD">)>>[16] <<HTML(</FONT>)>> <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> '''Epoching and averaging''' <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> |
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| ==== Epoching and averaging [Under construction] ==== <<HTML( )>>14. [[Tutorials/Epoching|Import epochs]] |
'''Source modeling''' |
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| <<HTML( )>>15. [[Tutorials/Averaging|Average response]] | <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] [Under construction] |
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| <<HTML( )>>16. [[Tutorials/ExploreRecordings|Exploring the average response]] | <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise covariance]] [Under construction] |
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| <<HTML( )>>17. 2D/3D topography | <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] [Under construction] |
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| <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] | <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] [Under construction] |
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| ==== Source modeling [Under construction] ==== <<HTML( )>>19. [[Tutorials/HeadModel|Head model]] |
'''Advanced signal processing''' |
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| <<HTML( )>>20. [[Tutorials/NoiseCovariance|Noise covariance]] | <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] [Under construction] |
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| <<HTML( )>>21. [[Tutorials/SourceEstimation|Source estimation]] | <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] [Under construction] |
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| <<HTML( )>>22. [[Tutorials/Scouts|Scouts]] | <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] [Under construction] |
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| ==== Advanced topics [Under construction] ==== <<HTML( )>>23. [[Tutorials/TimeFrequency|Time-frequency]] |
<<HTML( )>>27. Phase-amplitude coupling [Under construction] |
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| <<HTML( )>>24. [[Tutorials/Statistics|Statistics]] | '''Scripting''' |
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| <<HTML( )>>25. [[Tutorials/Connectivity|Connectivity]] | <<HTML( )>>28. [[Tutorials/Scripting|Complete tutorial script]] |
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| <<HTML( )>>26. Phase-amplitude coupling <<HTML( )>>27. [[Tutorials/Scripting|Advanced scripting]] <<HTML( )>>28. Complete tutorial script <<HTML( )>>29. Summary |
<<HTML( )>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]] |
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| == Complete analysis of other datasets == | == Other analysis scenarios == |
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| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory|MEG auditory tutorial]] | 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory|MEG auditory tutorial (CTF)]] |
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| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Resting|MEG resting state]] | 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Resting|MEG resting state (CTF)]] |
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| === Interface === | === Recordings === |
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| 1. ICA decomposition [Under construction] 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]] |
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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]] |
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| 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] | 1. [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] |
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| 1. Group studies: Averaging | 1. Group analysis: Averaging [Under construction] |
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=== Scripting === 1. [[SelectFiles|Selecting files in the database]] 1. [[Tutorials/TutRawScript|Full analysis with one script]] 1. [[Tutorials/TutUserProcess|How to write your own process]] |
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| === Functional connectivity === | === Advanced processing === |
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| === Statistics === | |
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| 1. [[Tutorials/TutUserProcess|How to write your own process]] | |
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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") |
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=== 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 |
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.
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. The number between brackets represents the number of printed pages for each tutorial.
| Starting a new study 1. Create a new protocol [9] 2. Import the subject anatomy [8] 3. Explore the anatomy [10] Reviewing 4. Channel file / MRI registration [11] 5. Continuous recordings [9] 6. Multiple windows [5] 7. Event markers [10] Pre-processing 8. Stimulation delays [10] 9. Select files / Run processes [10] 10. Power spectrum / Frequency filters [11] 11. Bad channels [6] 12. Artifact detection [7] 13. Artifact cleaning with SSP [16] 14. Additional bad segments [7] Epoching and averaging 15. Import epochs [7] 16. Average response [7] 17. Visual exploration [10] 18. Colormaps [6] 19. Clusters of sensors [4] | 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 |
Other analysis scenarios
MEG median nerve (CTF) [Under construction]
MEG median nerve (Elekta-Neuromag) [Under construction]
Advanced tutorials
Recordings
Montage editor [Under construction]
- ICA decomposition [Under construction]
Anatomy and registration
MRI segmentation: FreeSurfer, BrainSuite, BrainVISA, CIVET
Using the anatomy templates [Under construction]
- Group analysis: Averaging [Under construction]
Source modeling
Beamforming methods [Under construction]
Maximum Entropy on the Mean (MEM) [Under construction]
Advanced processing
Other useful how-to's
Tutorials from other authors
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 FJA tutorial in Japanese (click on the menu "Brainstorm")
?MEG analysis guidelines for McGill
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!