|
Size: 10208
Comment:
|
Size: 12992
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Tutorials = == How to use those tutorials == 1. Go through all the tutorials in the section ''Getting started with Brainstorm''. In just a few hours, they will introduce you to most of the main features of the application. 1. Then read more specific tutorials, closer to your personal interests. 1. If you want a printed version of a page, click on the "print" link on the top right of the page. == Getting started with Brainstorm == |
= 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 [[mailto:brainstorm@sipi.usc.edu|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 == 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: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]], * Slides from a selection of educational courses at [[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]], * Reference books: * 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. * [[Tutorials/BstFolders|0. Brainstorm architecture]] * [[Tutorials/TutFirstSteps|1. First steps]] * [[Tutorials/TutImportAnatomy|2. Importing individual anatomy]] * [[Tutorials/TutImportRecordings|3. Importing MEG recordings]] * [[Tutorials/TutExploreRecodings|4. Exploring the recordings]] * [[Tutorials/TutHeadModel|5. Head model]] * [[Tutorials/TutNoiseCov|6. Noise covariance]] * [[Tutorials/TutSourceEstimation|7. Source estimation]] * [[Tutorials/TutScouts|8. Scouts: Cortical regions of interest]] * [[Tutorials/TutProcesses|9. Processes: Graphical batching interface]] * [[Tutorials/TutStat|10. Statistics]] * [[Tutorials/TutTimefreq|11. Time-frequency]] == Advanced tutorials == === Processing continuous recordings === 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]] 1. [[Tutorials/TutMindNeuromag|Import and process raw recordings]] === Anatomy and registration === 1. [[CoordinateSystems|Brainstorm coordinate systems]] 1. [[Tutorials/SegBrainVisa|MRI segmentation: BrainVISA]] 1. [[Tutorials/LabelFreeSurfer|MRI segmentation: FreeSurfer]] 1. [[Tutorials/TutWarping|Warping default anatomy]] 1. [[Tutorials/TutDigitize|Digitize EEG electrodes locations and head shape]] === Source modeling === 1. [[Tutorials/TutBem|BEM with OpenMEEG]] 1. [[Tutorials/TutVolSource|Volumetric source estimation]] 1. [[Tutorials/TutXfit|Dipole models from Neuromag's Xfit]] 1. [[Tutorials/TutBEst|BrainEntropy MEM (Maximum Entropy on the Mean)]] === Other useful how-to's === 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] 1. [[Tutorials/TutScript|How to use Brainstorm without the GUI]] 1. [[Tutorials/KnownBugs|Known bugs]] == Get started (details) == |
| Line 10: | Line 74: |
| Line 11: | Line 76: |
| Line 25: | Line 91: |
| Line 27: | Line 94: |
| Line 28: | Line 96: |
| Line 29: | Line 98: |
| Line 30: | Line 100: |
| Line 31: | Line 102: |
| Line 32: | Line 104: |
| Line 33: | Line 106: |
| Line 35: | Line 109: |
| Line 36: | Line 111: |
| Line 37: | Line 113: |
| Line 38: | Line 115: |
| Line 40: | Line 118: |
| Line 41: | Line 120: |
| Line 42: | Line 122: |
| Line 43: | Line 124: |
| Line 44: | Line 126: |
| Line 45: | Line 128: |
| Line 46: | Line 130: |
| Line 47: | Line 132: |
| Line 48: | Line 134: |
| Line 49: | Line 136: |
| Line 50: | Line 138: |
| Line 52: | Line 141: |
| Line 53: | Line 143: |
| Line 54: | Line 145: |
| Line 55: | Line 147: |
| Line 56: | Line 149: |
| Line 58: | Line 152: |
| Line 59: | Line 154: |
| Line 61: | Line 157: |
| Line 62: | Line 159: |
| Line 63: | Line 161: |
| Line 64: | Line 163: |
* [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation#Project_sources_on_default_anatomy|Project sources on default anatomy]] |
|
| Line 66: | Line 168: |
| Line 67: | Line 170: |
| Line 68: | Line 172: |
| Line 69: | Line 174: |
| Line 70: | Line 176: |
| Line 71: | Line 178: |
| Line 73: | Line 181: |
| Line 74: | Line 183: |
| Line 75: | Line 185: |
| Line 77: | Line 188: |
| Line 78: | Line 190: |
| Line 79: | Line 192: |
| Line 81: | Line 195: |
| Line 82: | Line 197: |
| Line 83: | Line 199: |
| Line 84: | Line 201: |
| Line 85: | Line 203: |
| Line 86: | Line 205: |
| Line 87: | Line 207: |
| Line 88: | Line 209: |
| Line 89: | Line 211: |
| Line 90: | Line 213: |
| Line 91: | Line 215: |
== Advanced tutorials == === Continuous Neuromag recordings === 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]] 1. [[Tutorials/TutMindNeuromag|Import and process raw recordings]] === Anatomy and registration === 1. [[CoordinateSystems|Brainstorm coordinate systems]] 1. [[Tutorials/SegBrainVisa|MRI segmentation with BrainVISA]] 1. [[Tutorials/SegBrainVisa|MRI segmentation]][[Tutorials/SegBrainVisa|with BrainSuite]] 1. [[Tutorials/SegBrainVisa|MRI segmentation]][[Tutorials/SegBrainVisa|with FreeSurfer]] 1. [[Tutorials/TutRefineReg|Refine registration using head points]] 1. [[Tutorials/TutWarping|Warping default anatomy]] === Source estimation === 1. [[Tutorials/TutBem|BEM head model]] 1. [[Tutorials/TutVolSource|Volume source estimation]] 1. [[Tutorials/TutProject|Project sources on default anatomy]] 1. [[Tutorials/TutXfit|Import and visualize dipoles from Neuromag Xfit]] 1. [[Tutorials/TutClusters|Clusters of sensors]] === Other useful how-to's === 1. [[Tutorials/TutScript|How to use Brainstorm without the GUI]] 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] 1. [[Tutorials/TutCompile|How to compile Brainstorm]] 1. [[Tutorials/TutUserProcess|How to write your own processes]] 1. [[Tutorials/KnownBugs|Known bugs]] |
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.
?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: Cortical regions of interest
?9. Processes: Graphical batching interface
?10. Statistics
?11. Time-frequency
Advanced tutorials
Processing continuous recordings
?Review raw recordings and edit markers
Anatomy and registration
Source modeling
?Dipole models from Neuromag's Xfit
Other useful how-to's
?How to use Brainstorm without the GUI
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