Differences between revisions 45 and 202 (spanning 157 versions)

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: 978-0195307238
- Jean 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

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.

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.

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

Anatomy and registration

Graphical scripting

?Description of all the processes
Full analysis with one script
?How to write your own process

Source modeling

BEM with OpenMEEG
Volumetric source estimation
?Dipole models from Neuromag's Xfit and CTF's DipoleFit

Other types of recordings

Neuromag raw recordings [Not up to date]

Other useful how-to's

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. In just a few hours, they will introduce you to most of the main features of the application.
+= 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.
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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.
+== 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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-== Getting started with Brainstorm ==
=== Dataset description ===
The dataset that will be used for tutorials #2 to #10 is a somatotopy experiment recorded with a CTF 151 MEG system.
+ * A non-technical overview of MEG and EEG, with an emphasis on source modeling: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]],
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-Please download bst_sample_ctf.zip from the [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] section. Unzip it in a folder you will dedicate to original data. It can be anywhere but __not__ in the Brainstorm database or program folder. Example:
+ * Slides from a selection of educational courses at [[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]],
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- * __Windows__: My documents\MEG\sample_ctf\
 * __Linux__: /home/username/MEG/sample_ctf/
 * __MacOS__: Documents/MEG/sample_ctf/
+ * 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
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-||<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).<<BR>>- Cortex and head surfaces extracted with BrainVISA software([[Tutorials/SegBrainVisa|see tutorial]]) ||
||<style="vertical-align: top;">Datasets directory: ||- somMGYO-18av.ds: average response for the stimulation of the right thumb (one subject, 400 trials) .<<BR>>- 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. ||
+  * 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]].
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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).
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-=== Step by step tutorials ===
 * [[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]]
+Now you are well equipped to go through the software tutorial, '' Enjoy! ''
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-== Other useful tutorials ==
 1. [[Tutorials/SegBrainVisa|Extract head and cortex surface with BrainVISA]]
 1. [[Tutorials/SegBrainSuite|Extract head and cortex surface with BrainSuite]]
 1. [[Tutorials/SegFreeSurfer|Extract head and cortex surface with FreeSurfer]]
 1. [[Tutorials/TutInverseExpertMode|More inverse methods]]
 1. [[CiteBrainstorm|Cite Brainstorm in your publications]]
+== Get started ==
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.

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.

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

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

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

=== Graphical scripting ===
 1. [[Tutorials/RefProcesses|Description of all the processes]]
 1. [[Tutorials/TutRawScript|Full analysis with one script]]
 1. [[RefWriteProcess|How to write your own process]]

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

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

 1. [[Tutorials/TutXfit|Dipole models from Neuromag's Xfit and CTF's DipoleFit]]

=== Other types of recordings ===
 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]] [Not up to date]

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

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

=== 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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