Differences between revisions 116 and 157 (spanning 41 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: 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
Import and process raw recordings
Automated processing: a full analysis as a script

Anatomy and registration

Source modeling

Boundary Element Modeling (BEM)
Source estimation not constrained to cortical surface
?Import and visualize dipole models from another software (Neuromag's Xfit)
?BrainEntropy MEM (Maximum Entropy on the Mean)

Other useful how-to's

How to cite Brainstorm in your publications
?How to use Brainstorm without the GUI
?How to compile Brainstorm
Known bugs

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
- Compute from recordings
- Noise covariance from another dataset
?7. Source estimation
?8. Scouts: Cortical regions of interest
?9. Processes: Graphical batching interface
?10. Statistics
?11. Time-frequency

-  ⇤ ← Revision 116 as of 2011-12-20 22:37:59 → 
  Size: 12824
  Editor: grumio
  Comment:
+   ← Revision 157 as of 2012-08-13 22:25:18 → ⇥
  Size: 13221
  Editor: wpa162007
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= 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 a editor of this wiki. Please [[mailto:brainstorm@sipi.usc.edu|email us]] if you would like to contribute.
+= 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 ==
-Line 6:
+Line 9:
- * Non-technical overview of MEG and EEG, with an emphasis on source modeling and imaging: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]],
+ * A non-technical overview of MEG and EEG, with an emphasis on source modeling: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]],
-Line 8:
+Line 12:
-Line 9:
+Line 14:
- . * Peter Hansen, Morten Kringelbach, and Riitta Salmelin (Eds)
 [[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
  . * The following book features an extensive introduction to MEG:
  . * [[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 Library of Psychology), (Sept 2011) Jean Decety (Editor), John T. Cacioppo (Editor), ISBN-10: 019534216X, 1128 pages.
  . * A draft version of the chapter can be found [[attachment:Baillet_MEG Draft.pdf|here]].

Now you are well equipped to go through the software tutorial. Enjoy!

== Tutorial Guidelines ==
 1. Go through the 12 steps of ''Getting started with Brainstorm'' (see below). In just a few hours, you will be introduced to the essential features of the application.
 1. Read more specific tutorials (see ''Advanced Tutorials'' below), related to your personal interests/needs.
 1. If you need a printed version of a page, click on the "print" link at the top-right corner of the page.

== 12 easy steps through Brainstorm ==
+  * 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.
-Line 29:
+Line 32:
- * [[Tutorials/TutHeadModel|5. Computing a head model]]
 * [[Tutorials/TutNoiseCov|6. Computing a noise covariance matrix]]
+ * [[Tutorials/TutHeadModel|5. Head model]]
 * [[Tutorials/TutNoiseCov|6. Noise covariance]]
-Line 38:
+Line 41:
-=== Exploring Continuous Recordings ===
+=== Processing continuous recordings ===
-Line 41:
+Line 44:
+. [[Tutorials/TutFullAnalysis|Automated processing: a full analysis as a script]]
-Line 45:
+Line 49:
-. [[Tutorials/SegBrainSuite|MRI segmentation with BrainSuite]]
+. [[Tutorials/LabelFreeSurfer|FreeSurfer cortical parcellation]]
-Line 47:
+Line 53:
+. [[Tutorials/TutDigitize|Digitize EEG electrodes locations and head shape]]
-Line 50:
+Line 58:
-Line 51:
+Line 60:
-Line 52:
+Line 62:
-Line 56:
+Line 67:
-Line 57:
+Line 69:
-Line 58:
+Line 71:
-Line 60:
+Line 74:
-== Getting started (details) ==
+== Get started (details) ==
-Line 63:
+Line 77:
-Line 64:
+Line 79:
-Line 78:
+Line 94:
-Line 80:
+Line 97:
-Line 81:
+Line 99:
-Line 82:
+Line 101:
-Line 83:
+Line 103:
-Line 84:
+Line 105:
-Line 85:
+Line 107:
-Line 86:
+Line 109:
-Line 88:
+Line 112:
-Line 89:
+Line 114:
-Line 90:
+Line 116:
-Line 91:
+Line 118:
-Line 93:
+Line 121:
-Line 94:
+Line 123:
-Line 95:
+Line 125:
-Line 96:
+Line 127:
-Line 97:
+Line 129:
-Line 98:
+Line 131:
-Line 99:
+Line 133:
-Line 100:
+Line 135:
-Line 101:
+Line 137:
-Line 102:
+Line 139:
-Line 103:
+Line 141:
-Line 105:
+Line 144:
-Line 106:
+Line 146:
-Line 107:
+Line 148:
-Line 108:
+Line 150:
-Line 109:
+Line 152:
-Line 111:
+Line 155:
-Line 112:
+Line 157:
-Line 114:
+Line 160:
-Line 115:
+Line 162:
-Line 116:
+Line 164:
-Line 117:
+Line 166:
-Line 118:
+Line 168:
-Line 120:
+Line 171:
-Line 121:
+Line 173:
-Line 122:
+Line 175:
-Line 123:
+Line 177:
-Line 124:
+Line 179:
-Line 125:
+Line 181:
-Line 127:
+Line 184:
-Line 128:
+Line 186:
-Line 129:
+Line 188:
-Line 131:
+Line 191:
-Line 132:
+Line 193:
-Line 133:
+Line 195:
-Line 135:
+Line 198:
-Line 136:
+Line 200:
-Line 137:
+Line 202:
-Line 138:
+Line 204:
-Line 139:
+Line 206:
-Line 140:
+Line 208:
-Line 141:
+Line 210:
-Line 142:
+Line 212:
-Line 143:
+Line 214:
-Line 144:
+Line 216:

Software

Users

Development