|
Size: 10174
Comment:
|
Size: 12859
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 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. However, note that those pages are updated with the software, and cannot be kept as long term reference documentation. * [[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]] * [[Tutorials/TutProcesses|9. Scripting]] * [[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/LabelFreeSurfer|MRI segmentation: FreeSurfer]] 1. [[Tutorials/SegBrainVisa|MRI segmentation: BrainVISA]] 1. [[Tutorials/TutWarping|Warping default anatomy]] 1. [[Tutorials/TutDigitize|Digitize EEG electrodes 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]] === Other useful how-to's === 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] 1. [[Tutorials/KnownBugs|Known bugs]] == Get started (details) == |
| Line 10: | Line 69: |
| Line 11: | Line 71: |
| Line 25: | Line 86: |
| Line 27: | Line 89: |
| Line 28: | Line 91: |
| Line 29: | Line 93: |
| Line 30: | Line 95: |
| Line 31: | Line 97: |
| Line 32: | Line 99: |
| Line 33: | Line 101: |
| * [[Tutorials/TutImportRecordings|3. Importing recordings]] | * [[Tutorials/TutImportRecordings|3. Importing MEG recordings]] |
| Line 35: | Line 104: |
| Line 36: | Line 106: |
| Line 37: | Line 108: |
| Line 38: | Line 110: |
| Line 40: | Line 113: |
| Line 41: | Line 115: |
| Line 42: | Line 117: |
| Line 43: | Line 119: |
| Line 44: | Line 121: |
| Line 45: | Line 123: |
| Line 46: | Line 125: |
| Line 47: | Line 127: |
| Line 48: | Line 129: |
| Line 49: | Line 131: |
| Line 50: | Line 133: |
| Line 52: | Line 136: |
| Line 53: | Line 138: |
| Line 54: | Line 140: |
| Line 55: | Line 142: |
| Line 56: | Line 144: |
| Line 58: | Line 147: |
| Line 59: | Line 149: |
| Line 61: | Line 152: |
| Line 62: | Line 154: |
| Line 63: | Line 156: |
| Line 64: | Line 158: |
* [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation#Project_sources_on_default_anatomy|Project sources on default anatomy]] |
|
| Line 66: | Line 163: |
| Line 67: | Line 165: |
| Line 68: | Line 167: |
| Line 69: | Line 169: |
| Line 70: | Line 171: |
| Line 71: | Line 173: |
| Line 73: | Line 176: |
| Line 74: | Line 178: |
| Line 75: | Line 180: |
| Line 77: | Line 183: |
| Line 78: | Line 185: |
| Line 79: | Line 187: |
| Line 81: | Line 190: |
| Line 82: | Line 192: |
| Line 83: | Line 194: |
| Line 84: | Line 196: |
| Line 85: | Line 198: |
| Line 86: | Line 200: |
| Line 87: | Line 202: |
| Line 88: | Line 204: |
| Line 89: | Line 206: |
| Line 90: | Line 208: |
| Line 91: | Line 210: |
== Advanced tutorials == === 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]] === Recordings === 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]] 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]] === 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. 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. Scripting
?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
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