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| = Tutorials = The following pages will take you through a typical workflow of data analyses that will feature most of the tools and applications of Brainstorm. We are updating these pages constantly, keeping up with new developments and features in the software: you are therefore welcome to [[mailto:brainstorm@sipi.usc.edu|suggest]] improvements and additions but also to contribute by becoming a editor of this wiki. Please [[mailto:brainstorm@sipi.usc.edu|email us]] if you would like to contribute. |
= Brainstorm Tutorials = The following pages will take you through a typical workflow of data analyses that will feature most of the tools and applications of Brainstorm. We are updating these pages constantly, keeping up with new developments and features in the software. You are therefore welcome to suggest improvements and additions but also to contribute by becoming an editor of this wiki. Please [[mailto:brainstorm@sipi.usc.edu|email us]] if you would like to contribute. == Required background == |
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| * Non-technical overview of MEG and EEG, with an emphasis on source modeling and imaging: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]], | * A non-technical overview of MEG and EEG, with an emphasis on source modeling: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]], |
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. * Peter Hansen, Morten Kringelbach, and Riitta Salmelin (Eds) [[http://www.amazon.com/MEG-Introduction-Methods-Peter-Hansen/dp/0195307232/ref=sr_1_1?ie=UTF8&qid=1324419425&sr=8-1|MEG: An Introduction to Methods]] Oxford University Press; (29 July 2010); 448 pages; ISBN-13: 978-0195307238 . * The following book features an extensive introduction to MEG: . * [[http://www.amazon.com/Oxford-Handbook-Neuroscience-Library-Psychology/dp/019534216X/ref=sr_1_3?s=books&ie=UTF8&qid=1324419480&sr=1-3|The Oxford Handbook of Social Neuroscience]] (Oxford Library of Psychology), (Sept 2011) Jean Decety (Editor), John T. Cacioppo (Editor), ISBN-10: 019534216X, 1128 pages.* A draft version of the chapter can be found [[attachment:Baillet_MEG Draft.pdf|here]]. * A draft version of the chapter can be found [[attachment:Baillet_MEG Draft.pdf|here]]. Now you are well equipped to go through the software tutorial. Enjoy! == Tutorial Guidelines == 1. Go through the 12 steps of ''Getting started with Brainstorm'' (see below). In just a few hours, you will be introduced to the essential features of the application. 1. Read more specific tutorials (see ''Advanced Tutorials'' below), related to your personal interests/needs. 1. If you need a printed version of a page, click on the "print" link at the top-right corner of the page. == 12 easy steps through Brainstorm == |
* Peter Hansen, Morten Kringelbach, and Riitta Salmelin (Eds)<<BR>>[[http://www.amazon.com/MEG-Introduction-Methods-Peter-Hansen/dp/0195307232/ref=sr_1_1?ie=UTF8&qid=1324419425&sr=8-1|MEG: An Introduction to Methods]], ''Oxford University Press'', (29 July 2010), 448 pages, ISBN-13: 978-0195307238 * Jean Decety & John T. Cacioppo (Eds)<<BR>>[[http://www.amazon.com/Oxford-Handbook-Neuroscience-Library-Psychology/dp/019534216X/ref=sr_1_3?s=books&ie=UTF8&qid=1324419480&sr=1-3|The Oxford Handbook of Social Neuroscience]]'', Oxford University Press'', (Sept 2011), 1128 pages, ISBN-10: 019534216X.<<BR>>A draft version of the MEG chapter by Sylvain Baillet can be found [[attachment:BailletMEGDraft.pdf|here]]. * You can also ask us to come and organize a [[Training|training session]] at your institution, or [[http://www.bic.mni.mcgill.ca/ResearchLabsNeuroSPEED/HomePage|visit us]] to obtain training (!McGill's Montreal Neurological Institute). Now you are well equipped to go through the software tutorial, '' Enjoy! '' == Get started: 12 easy steps through Brainstorm == The easiest way to get started with Brainstorm is to follow carefully those 12 introduction tutorials. In just a few hours, you will be introduced to the essential features of the application. If you need a printed version of a page, click on the "print" link at the top-right corner of the page. However, note that those pages are updated with the software, and cannot be kept as long term reference documentation. |
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| * [[Tutorials/TutHeadModel|5. Computing a head model]] * [[Tutorials/TutNoiseCov|6. Computing a noise covariance matrix]] |
* [[Tutorials/TutHeadModel|5. Head model]] * [[Tutorials/TutNoiseCov|6. Noise covariance]] |
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| * [[Tutorials/TutScouts|8. Scouts: Cortical regions of interest]] * [[Tutorials/TutProcesses|9. Processes: Graphical batching interface]] |
* [[Tutorials/TutScouts|8. Scouts]] * [[Tutorials/TutProcesses|9. Graphical scripting]] |
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| === Exploring Continuous Recordings === 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]] 1. [[Tutorials/TutMindNeuromag|Import and process raw recordings]] |
=== Processing continuous recordings === 1. [[Tutorials/TutRawViewer|Review continuous recordings]] 1. [[Tutorials/TutRawSsp|Artifact cleaning (SSP)]] 1. [[Tutorials/TutRawAvg|Epoching and averaging]] === Other types of recordings === 1. EEG and Epilepsy 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]] 1. Comparison with !FieldTrip |
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| 1. [[Tutorials/SegBrainVisa|MRI segmentation with BrainVISA]] 1. [[Tutorials/SegBrainSuite|MRI segmentation with BrainSuite]] |
1. [[Tutorials/LabelFreeSurfer|MRI segmentation: FreeSurfer]] 1. [[Tutorials/SegBrainVisa|MRI segmentation: BrainVISA]] |
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| 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] === Graphical batching === 1. Description of all the processes 1. How to write your own process |
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| 1. [[Tutorials/TutBem|Boundary Element Modeling (BEM)]] 1. [[Tutorials/TutVolSource|Source estimation not constrained to cortical surface]] 1. [[Tutorials/TutXfit|Import and visualize dipole models from another software (Neuromag's Xfit]]) 1. [[Tutorials/TutMem|BrainEntropy MEM (Maximum Entropy on the Mean)]] |
1. [[Tutorials/TutBem|BEM with OpenMEEG]] 1. [[Tutorials/TutVolSource|Volumetric source estimation]] 1. [[Tutorials/TutXfit|Dipole models from Neuromag's Xfit]] |
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| 1. [[Tutorials/TutScript|How to use Brainstorm without the GUI]] 1. [[Tutorials/TutCompile|How to compile Brainstorm]] |
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| == Getting started (details) == | == Get started (details) == |
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Brainstorm Tutorials
The following pages will take you through a typical workflow of data analyses that will feature most of the tools and applications of Brainstorm. We are updating these pages constantly, keeping up with new developments and features in the software.
You are therefore welcome to suggest improvements and additions but also to contribute by becoming an editor of this wiki. Please email us if you would like to contribute.
Required background
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: here,
Slides from a selection of educational courses at megcommunity.org,
- Reference books:
Peter Hansen, Morten Kringelbach, and Riitta Salmelin (Eds)
MEG: An Introduction to Methods, Oxford University Press, (29 July 2010), 448 pages, ISBN-13: 978-0195307238Jean Decety & John T. Cacioppo (Eds)
The Oxford Handbook of Social Neuroscience, Oxford University Press, (Sept 2011), 1128 pages, ISBN-10: 019534216X.
A draft version of the MEG chapter by Sylvain Baillet can be found here.
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!
Get started: 12 easy steps through Brainstorm
The easiest way to get started with Brainstorm is to follow carefully those 12 introduction tutorials. In just a few hours, you will be introduced to the essential features of the application.
If you need a printed version of a page, click on the "print" link at the top-right corner of the page. However, note that those pages are updated with the software, and cannot be kept as long term reference documentation.
?0. Brainstorm architecture
?1. First steps
?2. Importing individual anatomy
?3. Importing MEG recordings
?4. Exploring the recordings
?5. Head model
?6. Noise covariance
?7. Source estimation
?8. Scouts
?9. Graphical scripting
?10. Statistics
?11. Time-frequency
Advanced tutorials
Processing continuous recordings
Other types of recordings
- EEG and Epilepsy
Comparison with FieldTrip
Anatomy and registration
Graphical batching
- Description of all the processes
- How to write your own process
Source modeling
?Dipole models from Neuromag's Xfit
Other useful how-to's
Get started (details)
?0. Brainstorm architecture
?1. First steps
?2. Importing individual anatomy
?3. Importing MEG recordings
?4. Exploring the recordings
?5. Computing a head model
?6. Computing a noise covariance matrix
?7. Source estimation
?8. Scouts: Cortical regions of interest
?9. Processes: Graphical batching interface
?10. Statistics
?11. Time-frequency