|
Size: 12714
Comment:
|
Size: 13148
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = 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 == |
| Line 6: | Line 9: |
| * 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]], |
| Line 8: | Line 12: |
| Line 9: | Line 14: |
. * 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 here. == 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. |
| Line 27: | Line 32: |
| * [[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]] |
| Line 30: | Line 35: |
| * [[Tutorials/TutScouts|8. Scouts: Cortical regions of interest]] * [[Tutorials/TutProcesses|9. Processes: Graphical batching interface]] |
* [[Tutorials/TutScouts|8. Scouts]] * [[Tutorials/TutProcesses|9. Graphical scripting]] |
| Line 36: | Line 41: |
| === 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 |
| Line 42: | Line 53: |
| 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]] |
| Line 46: | Line 58: |
| 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] === Graphical batching === 1. Description of all the processes 1. How to write your own process |
|
| Line 47: | Line 65: |
| 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]] |
| Line 54: | Line 73: |
| 1. [[Tutorials/TutScript|How to use Brainstorm without the GUI]] 1. [[Tutorials/TutCompile|How to compile Brainstorm]] |
|
| Line 58: | Line 76: |
| == Getting started (details) == | == Get started (details) == |
| Line 61: | Line 79: |
| Line 62: | Line 81: |
| Line 76: | Line 96: |
| Line 78: | Line 99: |
| Line 79: | Line 101: |
| Line 80: | Line 103: |
| Line 81: | Line 105: |
| Line 82: | Line 107: |
| Line 83: | Line 109: |
| Line 84: | Line 111: |
| Line 86: | Line 114: |
| Line 87: | Line 116: |
| Line 88: | Line 118: |
| Line 89: | Line 120: |
| Line 91: | Line 123: |
| Line 92: | Line 125: |
| Line 93: | Line 127: |
| Line 94: | Line 129: |
| Line 95: | Line 131: |
| Line 96: | Line 133: |
| Line 97: | Line 135: |
| Line 98: | Line 137: |
| Line 99: | Line 139: |
| Line 100: | Line 141: |
| Line 101: | Line 143: |
| Line 103: | Line 146: |
| Line 104: | Line 148: |
| Line 105: | Line 150: |
| Line 106: | Line 152: |
| Line 107: | Line 154: |
| Line 109: | Line 157: |
| Line 110: | Line 159: |
| Line 112: | Line 162: |
| Line 113: | Line 164: |
| Line 114: | Line 166: |
| Line 115: | Line 168: |
| Line 116: | Line 170: |
| Line 118: | Line 173: |
| Line 119: | Line 175: |
| Line 120: | Line 177: |
| Line 121: | Line 179: |
| Line 122: | Line 181: |
| Line 123: | Line 183: |
| Line 125: | Line 186: |
| Line 126: | Line 188: |
| Line 127: | Line 190: |
| Line 129: | Line 193: |
| Line 130: | Line 195: |
| Line 131: | Line 197: |
| Line 133: | Line 200: |
| Line 134: | Line 202: |
| Line 135: | Line 204: |
| Line 136: | Line 206: |
| Line 137: | Line 208: |
| Line 138: | Line 210: |
| Line 139: | Line 212: |
| Line 140: | Line 214: |
| Line 141: | Line 216: |
| Line 142: | Line 218: |
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