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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/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.<<BR>>Some sections are still being edited or under review: [[Tutorials/IntroductionReview|reviewing process]]. |
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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( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file & MRI coregistration]] | '''Reviewing''' |
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| <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] | <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
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| <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] | <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] | <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
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| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] [Under construction] | <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>9. [[Tutorials/ArtifactsFilter|Frequency filters]] [Under construction] | '''Pre-processing''' |
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| <<HTML( )>>10. [[Tutorials/BadChannels|Bad channels]] [Under construction] | <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>11. [[Tutorials/ArtifactsDetect|Artifact detection]] [Under construction] | <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>12. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] [Under construction] | <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
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| <<HTML( )>>13. [[Tutorials/BadSegments|Additional bad segments]] [Under construction] | <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> |
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| '''Epoching and averaging''' [Under construction] | <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
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| <<HTML( )>>14. [[Tutorials/Epoching|Import epochs]] | <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <<HTML(<FONT color="#DDDDDD">)>>[16] <<HTML(</FONT>)>> |
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| <<HTML( )>>15. [[Tutorials/Averaging|Average response]] <<HTML( )>>16. [[Tutorials/ExploreRecordings|Exploring the average response]] <<HTML( )>>17. 2D/3D topography <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] |
<<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
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| '''Source modeling''' [Under construction] | '''Epoching and averaging''' |
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| <<HTML( )>>19. [[Tutorials/HeadModel|Head model]] | <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
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| <<HTML( )>>20. [[Tutorials/NoiseCovariance|Noise covariance]] | <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
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| <<HTML( )>>21. [[Tutorials/SourceEstimation|Source estimation]] | <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| <<HTML( )>>22. [[Tutorials/Scouts|Scouts]] | <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> |
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| '''Advanced topics''' [Under construction] | <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> |
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| <<HTML( )>>23. [[Tutorials/TimeFrequency|Time-frequency]] | '''Source modeling''' |
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| <<HTML( )>>24. [[Tutorials/Statistics|Statistics]] | <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
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| <<HTML( )>>25. [[Tutorials/Connectivity|Connectivity]] | <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
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| <<HTML( )>>26. Phase-amplitude coupling | <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] [Under construction] |
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| <<HTML( )>>27. [[Tutorials/Scripting|Advanced scripting]] | <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>>[17] <<HTML(</FONT>)>> |
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| <<HTML( )>>28. Complete tutorial script | '''Advanced processing''' |
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| <<HTML( )>>29. Summary | <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[22] <<HTML(</FONT>)>> <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>>[25] <<HTML(</FONT>)>> [Under construction] <<HTML( )>>27. [[Tutorials/Workflows|Workflows]] [Under construction] <<HTML( )>>28. [[Tutorials/Scripting|Scripting]] [Under construction] |
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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]] |
== Other analysis scenarios == 1. [[Tutorials/Epilepsy|EEG and epilepsy]] 1. [[Tutorials/Auditory|MEG auditory tutorial (CTF)]] |
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| 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]] |
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] 1. [[Tutorials/Phantom|MEG current phantom (CTF)]] |
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| === Interface === | === Recordings === |
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| 1. [[Tutorials/ICA|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]] 1. [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] |
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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]] [Under construction] |
1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] |
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| 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] 1. Group studies: Averaging |
1. [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] |
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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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| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] [Under construction] |
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1. [[Tutorials/DipoleFitting|Dipole fitting with FieldTrip]] |
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| 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction] | 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] |
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| === Functional connectivity === | 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM) - Epilepsy]] === Advanced processing === 1. [[Tutorials/Connectivity|Functional connectivity]] [Under construction] |
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| === Statistics === | |
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| 1. [[Tutorials/Decoding|Decoding conditions (MVPA)]] 1. [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] 1. [[Tutorials/TutUserProcess|How to write your own process]] |
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| 1. [[Tutorials/IPythonNotebook|Brainstorm on IPython Notebook]] [Under construction] | |
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| 1. [[Tutorials/AllIntroduction|All the introduction tutorials on the same page]] === 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.
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.
Some sections are still being edited or under review: ?reviewing process.
| 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 [8] 21. Noise/data covariance [8] 22. Source estimation [Under construction] 23. Scouts [17] Advanced processing 24. Time-frequency [22] 25. Difference [9] 26. Statistics [25] [Under construction] 27. Workflows [Under construction] 28. Scripting [Under construction] |
Other analysis scenarios
MEG median nerve (CTF) [Under construction]
MEG median nerve (Elekta-Neuromag) [Under construction]
MEG visual single subject (Elekta-Neuromag) [Under construction]
MEG visual group study (Elekta-Neuromag) [Under construction]
?MEG current phantom (CTF)
Advanced tutorials
Recordings
Montage editor [Under construction]
?ICA decomposition [Under construction]
Anatomy and registration
MRI segmentation: FreeSurfer, BrainSuite, BrainVISA, CIVET
Source modeling
Deep cerebral structures [Under construction]
Beamforming methods [Under construction]
Advanced processing
Functional connectivity [Under construction]
Other useful how-to's
?Brainstorm on IPython Notebook [Under construction]
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!