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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 [[mailto:brainstorm@sipi.usc.edu|email us]] if you would like to contribute. |
= Tutorials = <<HTML(<FONT color="#888"><I>)>>We are currently working on a [[TutorialsNew|new version of this page]], expected to be finished during the summer 2015.<<HTML(</I></FONT>)>> |
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| * 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). | * 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). |
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| The easiest way to get started with Brainstorm is to follow carefully those 12+3 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 follow carefully these introduction tutorials. In just a few hours, you will be introduced to the essential features of the application. You will find a report form at the end of each tutorial, please share your comments to help us improve the documentation and the software. To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]]. |
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| You will find a report form at the end of each tutorial, please share your comments to help us improve the documentation and the software. 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. |
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 these pages are updated with the software, and cannot be kept as long term reference documentation. |
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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]] 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)]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/RatPac|Rat electrophysiology]] [Under construction] |
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| 1. MRI segmentation: * [[Tutorials/LabelFreeSurfer|FreeSurfer]] * [[Tutorials/SegBrainVisa|BrainVISA]] * [[Tutorials/SegBrainSuite|BrainSuite]] * [[Tutorials/SegCIVET|CIVET]] |
1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] |
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| 1. [[Tutorials/CoregisterSubjects|Group studies: Co-registering subjects]] | 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] |
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| 1. [[Tutorials/TutRealtime|Realtime head positioning in the CTF MEG system]] | 1. [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG system]] |
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| 1. [[Tutorials/RefProcesses|Description of all the processes]] | 1. [[SelectFiles|Selecting files in the database]] |
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| 1. [[RefWriteProcess|How to write your own process]] | 1. [[Tutorials/TutUserProcess|How to write your own process]] |
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| 1. [[Tutorials/TutVolSource|Volumetric source estimation]] | 1. [[Tutorials/TutVolSource|Volume source estimation]] |
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| 1. [[Tutorials/TutXfit|Dipole models from Neuromag's Xfit and CTF's DipoleFit]] | 1. [[Tutorials/TutDipScan|Computing and displaying dipoles]] |
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| === Other types of recordings === 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]] [Not up to date] |
1. [[Tutorials/Beamformers|Beamforming methods]] [Under construction] 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction] === Functional connectivity === 1. [[Tutorials/TutPac|Phase-amplitude coupling]] === Statistics === 1. [[ExportSpm8|Export volume source maps to SPM8 / SPM12]] 1. [[ExportSpm12|Export surface source maps to SPM12]] |
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| 1. [[CoordinateSystems|Coordinate systems]] | |
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| 1. [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]] 1. [[Tutorials/ArtifactDetect|Detecting bad segments in continuous recordings]] 1. [[Tutorials/MovementDetect|Detect subject movements]] 1. [[Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]] 1. [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm") |
Tutorials
We are currently working on a new version of this page, expected to be finished during the summer 2015.
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:
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!
Get started
The easiest way to get started with Brainstorm is to follow carefully these introduction tutorials. In just a few hours, you will be introduced to the essential features of the application. You will find a report form at the end of each tutorial, please share your comments to help us improve the documentation and the software. To get a quick overview of the software interface, you can watch this introduction video.
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 these pages are updated with the software, and cannot be kept as long term reference documentation.
12 easy steps through Brainstorm
?Brainstorm architecture [10 min]
?First steps [30 min]
?Importing individual anatomy [30 min]
?Importing MEG recordings [30 min]
?Exploring the recordings [60 min]
?Head model [30 min]
?Noise covariance [30 min]
?Source estimation [45 min]
?Scouts [45 min]
?Graphical scripting [45 min]
?Statistics [30 min]
?Time-frequency [1:30 hr]
Processing continuous recordings
?Review continuous recordings and edit markers [2:00 hr]
?Detect and remove artifacts [2:00 hr]
?Epoching and averaging [1:30 hr]
Advanced tutorials
Complete analysis of other datasets
Rat electrophysiology [Under construction]
Anatomy and registration
MRI segmentation: FreeSurfer, BrainSuite, BrainVISA, CIVET
Graphical scripting
Source modeling
Beamforming methods [Under construction]
Maximum Entropy on the Mean (MEM) [Under construction]
Functional connectivity
Statistics
Other useful how-to's
?MEG analysis guidelines for McGill
?Detecting bad segments in continuous recordings
A tutorial in Japanese (click on the menu "Brainstorm")
Examples
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 FJ