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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. |
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| '''Preparing the subject''' | <<HTML(<TABLE class="tuto-table"><TR><TD>)>> |
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| 1. [[Tutorials/CreateProtocol|Create a new protocol]] 1. [[Tutorials/ImportAnatomy|Import the subject anatomy]] 1. [[Tutorials/ExploreAnatomy|Explore the anatomy]] |
'''Starting a new study''' |
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| '''Reviewing and pre-processing''' | <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| 1. [[Tutorials/ChannelFile|Coregistration MEG-MRI]] [Under construction] 1. [[Tutorials/ReviewRaw|Review continuous files]] [Under construction] 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] 1. [[Tutorials/Desktop|Desktop]] 1. [[Tutorials/EventMarkers|Edit event markers]] 1. [[Tutorials/StimDelays|Fixing stimulation delays]] 1. [[Tutorials/ArtifactsFilter|Frequency filters]] 1. Bad channels 1. [[Tutorials/ArtifactsDetect|Detecting artifacts]] 1. [[Tutorials/ArtifactsSsp|Cleaning artifacts with SSP]] 1. [[Tutorials/BadChannels|Additional bad segments]] |
<<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
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| '''Epoching and averaging''' [Under construction] | <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
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| 1. [[Tutorials/Epoching|Epoching]] 1. [[Tutorials/Averaging|Averaging trials]] 1. [[Tutorials/ExploreRecordings|Explore the average response]] 1. [[Tutorials/Colormaps|Colormaps]] |
'''Reviewing''' |
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| '''Source modeling''' [Under construction] | <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
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| 1. [[Tutorials/HeadModel|Head model]] 1. [[Tutorials/NoiseCovariance|Noise covariance]] 1. [[Tutorials/SourceEstimation|Source estimation]] 1. [[Tutorials/Scouts|Scouts]] |
<<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
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| '''Advanced topics''' [Under construction] | <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
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| 1. [[Tutorials/TimeFrequency|Time-frequency]] 1. [[Tutorials/Statistics|Statistics]] 1. [[Tutorials/Connectivity|Connectivity]] 1. Phase-amplitude coupling 1. [[Tutorials/Scripting|Advanced scripting]] 1. Full script 1. Summary |
<<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<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 (CTF)]] 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)]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Resting|MEG resting state (CTF)]] |
'''Pre-processing''' <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<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>)>> <<HTML(</TD><TD>)>> '''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>)>> '''Source modeling''' <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[26] <<HTML(</FONT>)>> <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>>[17] <<HTML(</FONT>)>> '''Advanced processing''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[22] <<HTML(</FONT>)>> <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] [Under construction] <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] [Under construction] <<HTML( )>>27. [[Tutorials/Scripting|Scripting]] [Under construction] <<HTML(</TD></TR></TABLE>)>> == Other analysis scenarios == 1. [[Tutorials/Epilepsy|EEG and epilepsy]] 1. [[Tutorials/Auditory|MEG auditory tutorial (CTF)]] 1. [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] [Under construction] 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] |
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| === Recordings === 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] 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. [[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]] |
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| 1. [[Tutorials/MegCoreg|Co-registration of MEG runs]] [Under construction] | 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]] 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/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 === |
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| === Statistics === | |
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| 1. [[Tutorials/Decoding|Decoding conditions (MVPA)]] 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.
| 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 [26] 23. Scouts [17] Advanced processing 24. Time-frequency [22] 25. Statistics [Under construction] 26. Connectivity [Under construction] 27. 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]
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
Deep cerebral structures [Under construction]
Beamforming methods [Under construction]
Advanced processing
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!