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| = Tutorials = == Important notes == * Distribution: * In all the tutorials, we will consider that you are working with the source distribution of Brainstorm. * If you are running a stand-alone distribution: some menus might be missing, some indications might not applicable to you, but everything else should work the same way. * Before starting using Brainstorm with your own data: * You should go through '''__all the tutorials__''' in the following section: "''Getting started with Brainstorm''". In just a few hours, they will introduce you to most of the main features of the application. * Then you can read more specific tutorials, closer to your personal interests. * 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, and go to the next tutorial. |
= 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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| == 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. |
== 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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| 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: | * 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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| * __Windows__: My documents\MEG\sample_ctf\ * __Linux__: /home/username/MEG/sample_ctf/ * __MacOS__: Documents/MEG/sample_ctf/ |
* 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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| ||<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. || |
* 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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| * [[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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| === 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]] * [[Tutorials/TutStat|10. Statistics]] * [[Tutorials/TutTimefreq|11. Time-frequency]] |
* [[http://www.ncbi.nlm.nih.gov/pubmed/23046981|Good practice for conducting and reporting MEG research]], Gross et al, Neuroimage, 2013 |
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| == Other useful tutorials == 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]] 1. [[Tutorials/TutMindNeuromag|Import and process Neuromag raw recordings]] 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/TutImportRaw|Import and epoch continuous recordings]] 1. [[Tutorials/TutInverseExpertMode|More inverse methods]] 1. [[Tutorials/TutScript|Using Brainstorm without the GUI]] 1. [[CiteBrainstorm|Cite Brainstorm in your publications]] |
* 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 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 == === More acquisition systems === 1. [[Tutorials/Epilepsy|EEG and epilepsy]] 1. [[Tutorials/TutMindNeuromag|Elekta-Neuromag recordings]] [Not up to date] === Anatomy and registration === 1. [[CoordinateSystems|Brainstorm coordinate systems]] 1. MRI segmentation:[[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainSuite|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|Realtime head positioning in the CTF MEG system]] === Graphical scripting === 1. [[SelectFiles|Selecting files in the database]] 1. [[Tutorials/RefProcesses|Description of all the processes]] 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|Volumetric source estimation]] 1. [[Tutorials/TutDipScan|Computing and Displaying Dipoles]] === 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. [[CoordinateSystems|Coordinate systems]] 1. [[Tutorials/KnownBugs|Known bugs]] 1. [[Tutorials/WorkflowGuide|MEG analysis guidelines for McGill]] === 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 |
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:
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 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
More acquisition systems
Elekta-Neuromag recordings [Not up to date]
Anatomy and registration
MRI segmentation:FreeSurfer, BrainVISA, BrainSuite, CIVET
Graphical scripting
?Description of all the processes
Source modeling
Functional connectivity
Statistics
Other useful how-to's
?MEG analysis guidelines for McGill
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