Differences between revisions 35 and 284 (spanning 249 versions)

Tutorials [2011-2014]

[WARNING: This page is part of the old tutorials, please refer to the new documentation]

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 Consortium
Slides 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 pages
- The 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

EEG and epilepsy
MEG auditory tutorial
MEG median nerve (Yokogawa/KIT)
MEG median nerve (Elekta-Neuromag)
MEG resting state (CTF)
Rat electrophysiology [Under construction]

Anatomy and registration

Graphical scripting

Source modeling

BEM with OpenMEEG
Volume source estimation
Computing and displaying dipoles
Beamforming methods [Under construction]
Maximum Entropy on the Mean (MEM) [Under construction]

Functional connectivity

Phase-amplitude coupling

Statistics

Other useful how-to's

How to cite Brainstorm in your publications
Known bugs
Cleaning artifacts using SSP: examples
?Detecting bad segments in continuous recordings
Detect subject movements
Real-time head-tracking for adjusting head position
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

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-= Tutorials =
== Important notes ==
 * In all the tutorials, we will consider that you are working with the source distribution of Brainstorm, as it is the recommanded way to use this toolbox.
 * If you are working with compiled binaries, some menus might be missing, but everything else should work the same way.
 * Before starting using Brainstorm with your own data, you should go through __all __the tutorials in "Getting started with Brainstorm" section.
+= Tutorials [2011-2014] =
'''[WARNING: This page is part of the old tutorials, please refer to the [[Tutorials|new documentation]]]'''<<BR>><<BR>><<BR>>
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-In just a few hours, they will introduce you to most of the main features of the application.
+== 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:
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- * If you want a printed version of this documentation:
  * Open a tutorial, go to the menu on top of the page,
  * Select ''More actions > Print view'', print the page,
  * Click on the ''Back ''button of your browser, and go to next tutorial.
+ * A non-technical overview of MEG and EEG, with an emphasis on source modeling:<<BR>> [[http://www.canada-meg-consortium.org/EN/MegIntro|Canada MEG Consortium]]
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-== Getting started with Brainstorm ==
=== Dataset description ===
You should already have downloaded this package if you have done correctly the previous tutorial. If it is not the case, go back to the [[Tutorials/TutImportAnatomy|previous tutorial]] and follow all the instructions to create the ''TutorialCTF ''protocol.
||<width="150px" style="vertical-align: top;">File: ||'''bst_sample_ctf.zip''' ||
||<style="vertical-align: top;">Acquisition system: ||CTF MEG, 151 axial gradiometers, La Salpetriere Hospital, Paris ||
||<style="vertical-align: top;">Protocol: ||Shuffled electrical stimulations of the thumb fingers from both hands. The idea is to get a map of the primary sensory response on the cortex ||
||<style="vertical-align: top;">Author: ||Data provided courtesy of Sabine Meunier ||
||<style="vertical-align: top;">Anatomy directory: ||- T1-MRI of the subject in CTF format (.mri). - Cortex and head surfaces extracted with BrainVISA software ||
||<style="vertical-align: top;">Datasets directory: ||- somMGYO-18av.ds: average response for the stimulation of the right thumb (one subject, 400 trials) . - somMDYO-18av.ds: average response for the stimulation of the left thumb (one subject, 400 trials) ||
||<style="vertical-align: top;">Observations: ||Stimulus occurs at time 0. There's a first tiny wave occuring at about 20ms or so but it's not too clear on all fingers. So if you are to compute cortical maps, start by the 40ms peak which is also of interest and which has much better SNR. ||
+ * Slides from a selection of educational courses:<<BR>>[[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]]
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+ * Reference books:
  * [[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]]<<BR>>Editors: P Hansen, M Kringelbach, R Salmelin, ''Oxford University Press'', 2010, 448 pages
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-=== Step by step tutorials ===
 * [[BstFolders|0. Introduction to Brainstorm structure]]
 * [[Tutorials/TutFirstSteps|1. First steps]]
 * [[Tutorials/TutImportAnatomy|2. Importing individual anatomy]]
 * [[Tutorials/TutImportRecordings|3. Importing recordings]]
 * [[Tutorials/TutExploreRecodings|4. Exploring the recordings]]
 * [[Tutorials/TutHeadModel|5. Computing a head model]]
 * [[Tutorials/TutNoiseCov|6. Computing a noise covariance matrix]]
 * [[Tutorials/TutSourceEstimation|7. Source estimation]]
 * [[Tutorials/TutScouts|8. Scouts: cortical regions of interest]]
 * [[Tutorials/TutProcesses|9. Processes: Graphical batching interface]]
+  * [[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]]<<BR>>Editors: J Decety, JT Cacioppo, ''Oxford University Press'', 2011, 1128 pages<<BR>>A draft version of the MEG chapter by Sylvain Baillet can be found [[attachment:BailletMEGDraft.pdf|here]]. '' ''
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-== Other useful tutorials ==
 1. [[CiteBrainstorm|Cite Brainstorm in your publications]]
+ * [[http://www.ncbi.nlm.nih.gov/pubmed/23046981|Good practice for conducting and reporting MEG research]], Gross et al, Neuroimage, 2013

 * 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 ==
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]].

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 ===
 1. [[Tutorials/BstFolders|Brainstorm architecture]]    ''[10 min] ''
 1. [[Tutorials/TutFirstSteps|First steps]]    ''[30 min]''
 1. [[Tutorials/TutImportAnatomy|Importing individual anatomy]]     ''[30 min]''
 1. [[Tutorials/TutImportRecordings|Importing MEG recordings]]     ''[30 min]''
 1. [[Tutorials/TutExploreRecodings|Exploring the recordings]]     ''[60 min]''
 1. [[Tutorials/TutHeadModel|Head model]]     ''[30 min]''
 1. [[Tutorials/TutNoiseCov|Noise covariance]]     ''[30 min]''
 1. [[Tutorials/TutSourceEstimation|Source estimation]]     ''[45 min]''
 1. [[Tutorials/TutScouts|Scouts]]     ''[45 min]''
 1. [[Tutorials/TutProcesses|Graphical scripting]]     ''[45 min]''
 1. [[Tutorials/TutStat|Statistics]]     ''[30 min]''
 1. [[Tutorials/TutTimefreq|Time-frequency]]     ''[1:30 hr'']

=== Processing continuous recordings ===
 1. [[Tutorials/TutRawViewer|Review continuous recordings and edit markers]] ''[2:00 hr]''
 1. [[Tutorials/TutRawSsp|Detect and remove artifacts]] ''[2:00 hr]''
 1. [[Tutorials/TutRawAvg|Epoching and averaging]] ''[1:30 hr]''

== Advanced tutorials ==
=== 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]

=== Anatomy and registration ===
 1. [[CoordinateSystems|Brainstorm coordinate systems]]
 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]]

 1. [[Tutorials/TutWarping|Warping default anatomy]]

 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]]

 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]]
 1. [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG system]]

=== Graphical scripting ===
 1. [[SelectFiles|Selecting files in the database]]
 1. [[Tutorials/TutRawScript|Full analysis with one script]]
 1. [[Tutorials/TutUserProcess|How to write your own process]]

=== Source modeling ===
 1. [[Tutorials/TutBem|BEM with OpenMEEG]]

 1. [[Tutorials/TutVolSource|Volume source estimation]]

 1. [[Tutorials/TutDipScan|Computing and displaying dipoles]]

 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]]

=== Other useful how-to's ===
 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]]

 1. [[Tutorials/KnownBugs|Known bugs]]

 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")

=== Examples ===
 1. This video illustrates how Brainstorm can be used for studying amygdala activity:<<BR>>[[http://www.jove.com/video/50212/how-to-detect-amygdala-activity-with-magnetoencephalography-using?status=a52218k|How to Detect Amygdala Activity with Magnetoencephalography using Source Imaging]] <<BR>>Authors: Balderston NL, Schultz DH, Baillet S, Helmstetter FJ

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