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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 [[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.

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 and imaging: [[http://www.canada-meg-consortium.org/EN/MegIntro|here]],

 *
 Slides from a selection of educational courses at [[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]],

 * Reference books:
  * 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 [[attachment:BailletMEGDraft.pdf|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), Oxford University Press'', (Sept 2011) Jean Decety & John T. Cacioppo (Eds), ISBN-10: 019534216X, 1128 pages.

   *
   A draft version of the MEG chapter by [[http://www.bic.mni.mcgill.ca/PeopleFaculty/BailletSylvain|Sylvain Baillet]] can be found [[attachment:BailletMEGDraft.pdf|here]].		 = 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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 *
 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).		 == 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:
Line 30: Line 9:
 * 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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Now you are well equipped to go through the software tutorial.'' Enjoy! ''  * 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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== Tutorial Guidelines ==
 1. Go through the following 12 steps to get started with Brainstorm. In just a few hours, you will be introduced to the essential features of the application.		  * 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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 Read more tutorials (see ''Advanced Tutorials'' below), that may be more specific to your personal interests/needs.   * [[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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 1. If you need a printed version of a page, click on the "print" link at the top-right corner of the page.  * [[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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== Get started: 12 easy steps through Brainstorm ==
 * [[Tutorials/BstFolders|0. Brainstorm architecture]]		  * 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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 * [[Tutorials/TutFirstSteps|1. First steps]] Now you are well equipped to go through the software tutorial, '' Enjoy! ''
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 *
 '''[[Tutorials/TutImportAnatomy|2. Importing individual anatomy]] '''		 == 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]].
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 *
 '''[[Tutorials/TutImportRecordings|3. Importing MEG recordings]] '''		 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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 *
 '''[[Tutorials/TutExploreRecodings|4. Exploring the recordings]] '''		 === 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'']
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 *
 '''[[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]] '''
 === 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]''
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=== Exploring Continuous Recordings ===
 1.
 '''[[Tutorials/TutRawViewer|Review raw recordings and edit markers]] '''		 === 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)]]
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 1.
 '''[[Tutorials/TutMindNeuromag|Import and process raw recordings]] '''
  1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/RatPac|Rat electrophysiology]] [Under construction]
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 1.
 '''[[CoordinateSystems|Brainstorm coordinate systems]] '''		  1. [[CoordinateSystems|Brainstorm coordinate systems]]
 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]]
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 1.
 '''[[Tutorials/SegBrainVisa|MRI segmentation with BrainVISA]] '''		  1. [[Tutorials/TutWarping|Warping default anatomy]]
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 1.
 '''[[Tutorials/SegBrainSuite|MRI segmentation with BrainSuite]] '''		  1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]]
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 1.
 '''[[Tutorials/TutWarping|Warping default anatomy]] '''		  1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]]
 1. [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG system]]
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=== 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]]
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 1.
 '''[[Tutorials/TutBem|Boundary Element Modeling (BEM)]] '''		  1. [[Tutorials/TutBem|BEM with OpenMEEG]]
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 1.
 '''[[Tutorials/TutVolSource|Source estimation not constrained to cortical surface]] '''		  1. [[Tutorials/TutVolSource|Volume source estimation]]
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 1.
 '''[[Tutorials/TutXfit|Import and visualize dipole models from another software (Neuromag's Xfit]]) '''		  1. [[Tutorials/TutDipScan|Computing and displaying dipoles]]
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 1.
 '''[[Tutorials/TutMem|BrainEntropy MEM (Maximum Entropy on the Mean)]] '''		  1. [[Tutorials/Beamformers|Beamforming methods]] [Under construction]
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 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.
 '''[[CiteBrainstorm|How to cite Brainstorm in your publications]] '''		  1. [[CiteBrainstorm|How to cite Brainstorm in your publications]]
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 1.
 '''[[Tutorials/TutScript|How to use Brainstorm without the GUI]] '''		  1. [[Tutorials/KnownBugs|Known bugs]]
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 1.
 '''[[Tutorials/TutCompile|How to compile Brainstorm]] '''		  1. [[Tutorials/WorkflowGuide|MEG analysis guidelines for McGill]]
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 1.
 '''[[Tutorials/KnownBugs|Known bugs]] '''		  1. [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]]
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 1. [[Tutorials/ArtifactDetect|Detecting bad segments in continuous recordings]]
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== Getting started (details) ==
 *
 '''[[Tutorials/BstFolders|0. Brainstorm architecture]] '''		  1. [[Tutorials/MovementDetect|Detect subject movements]]
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  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/BstFolders#Brainstorm_folders|Brainstorm folders]] '''		  1. [[Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]]
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  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/BstFolders#Brainstorm_database_.28concept.29|Brainstorm database (concept)]] '''		  1. [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm")
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  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/BstFolders#Brainstorm_database_.28files.29|Brainstorm database (files)]] '''



 *
 '''[[Tutorials/TutFirstSteps|1. First steps]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Create_first_protocol|Create first protocol]] '''


  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Fiducials_selection_.28MRI_Viewer.29|Fiducials selection (MRI Viewer)]] '''


  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Protocol_exploration|Protocol exploration]] '''


  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#MRI_visualization|MRI visualization]] '''


  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Surfaces_visualization|Surfaces visualization]] '''


  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Coordinates_tab|Coordinates tab]] '''


 *
 '''[[Tutorials/TutImportAnatomy|2. Importing individual anatomy]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportAnatomy#Dataset_description|Dataset description]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportAnatomy#Import_MRI|Import MRI]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportAnatomy#Import_surfaces|Import surfaces]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportAnatomy#Downsample_and_merge_surfaces|Downsample and merge surfaces]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportAnatomy#Check_registration_with_MRI|Check registration with MRI]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportAnatomy#Fix_registration_with_MRI|Fix registration with MRI]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportAnatomy#What_happened_on_the_hard_drive|What happened on the hard drive]] '''


 *
 '''[[Tutorials/TutImportRecordings|3. Importing MEG recordings]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportRecordings#Import_recordings|Import recordings]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportRecordings#Channel_file|Channel file]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportRecordings#MEG_recordings|MEG recordings]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportRecordings#Managing_conditions|Managing conditions]] '''


 *
 '''[[Tutorials/TutExploreRecodings|4. Exploring the recordings]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Display_recordings|Display recordings]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Time_exploration|Time exploration]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Sensors_selection|Sensors selection]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Time_series_in_columns|Time series in columns]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Time_selection|Time selection]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Good_.2BAC8_bad_channels|Good / bad channels]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Colormap_configuration|Colormap configuration]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Toolbar_.2BAC8_Manipulating_multiple_windows|Toolbar / Manipulating multiple windows]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Database_navigator|Database navigator]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Snapshots|Snapshots]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings#Keyboard_shortcuts|Keyboard shortcuts]] '''


 *
 '''[[Tutorials/TutHeadModel|5. Computing a head model]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutHeadModel#Forward_problem|Forward problem]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutHeadModel#Single_sphere_model|Single sphere model]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutHeadModel#Overlapping_spheres_model|Overlapping spheres model]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutHeadModel#Selection_of_a_head_model|Selection of a head model]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutHeadModel#Batching_head_model_computation|Batching head model computation]] '''


 *
 '''[[Tutorials/TutNoiseCov|6. Computing a noise covariance matrix]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutNoiseCov#Compute_from_recordings|Compute from recordings]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutNoiseCov#Noise_covariance_from_another_dataset|Noise covariance from another dataset]] '''


 *
 '''[[Tutorials/TutSourceEstimation|7. Source estimation]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation#Computing_sources_for_a_single_data_file|Computing sources for a single data file]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation#Sources_visualization|Sources visualization]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation#Computing_sources_for_multiple_data_files|Computing sources for multiple data files]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation#Minimum_norm_options|Minimum norm options]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation#Project_sources_on_default_anatomy|Project sources on default anatomy]] '''


 *
 '''[[Tutorials/TutScouts|8. Scouts: Cortical regions of interest]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutScouts#Creating_a_scout|Creating a scout]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutScouts#Scout_function|Scout function]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutScouts#Multiple_scouts|Multiple scouts]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutScouts#Load.2BAC8-save_scouts|Load/save scouts]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutScouts#Display_scouts_time_series_from_the_database_tree|Display scouts time series from the database tree]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutScouts#Scout_toolbar_and_menus|Scout toolbar and menus]] '''


 *
 '''[[Tutorials/TutProcesses|9. Processes: Graphical batching interface]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutProcesses#Selecting_files_to_process|Selecting files to process]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutProcesses#Creating_a_pipeline|Creating a pipeline]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutProcesses#Another_example:_z-score_and_scouts|Another example: z-score and scouts]] '''


 *
 '''[[Tutorials/TutStat|10. Statistics]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutStat#Binary_processes|Binary processes]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutStat#Warning:_Mixing_recordings_from_different_runs|Mixing recordings from different runs]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutStat#Tests|Tests]] '''


 *
 '''[[Tutorials/TutTimefreq|11. Time-frequency]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#Introduction_to_complex_Morlet_wavelets|Introduction to complex Morlet wavelets]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#Edge_effects|Edge effects]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#TF:_Recordings|TF: Recordings]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#Description_of_the_options|Description of the options]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#Display_time-frequency_maps|Display time-frequency maps]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#Contents_of_the_.22timefreq.22_files|Contents of the "timefreq" files]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#Time_and_frequency_bands|Time and frequency bands]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#TF:_Clusters_time_series|TF: Clusters time series]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#TF:_Cortical_sources|TF: Cortical sources]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#TF:_Scouts_time_series|TF: Scouts time series]] '''

  *
  '''[[http://neuroimage.usc.edu/brainstorm/Tutorials/TutTimefreq#Processing_time-frequency_files|Processing time-frequency files]] '''		 === 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

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

  1. ?Brainstorm architecture [10 min]

  2. ?First steps [30 min]

  3. ?Importing individual anatomy [30 min]

  4. ?Importing MEG recordings [30 min]

  5. ?Exploring the recordings [60 min]

  6. ?Head model [30 min]

  7. ?Noise covariance [30 min]

  8. ?Source estimation [45 min]

  9. ?Scouts [45 min]

  10. ?Graphical scripting [45 min]

  11. ?Statistics [30 min]

  12. ?Time-frequency [1:30 hr]

Processing continuous recordings

  1. ?Review continuous recordings and edit markers [2:00 hr]

  2. ?Detect and remove artifacts [2:00 hr]

  3. ?Epoching and averaging [1:30 hr]

Advanced tutorials

Complete analysis of other datasets

  1. EEG and epilepsy

  2. MEG auditory tutorial

  3. MEG median nerve (Yokogawa/KIT)

  4. MEG median nerve (Elekta-Neuromag)

  5. MEG resting state (CTF)

  6. Rat electrophysiology [Under construction]

Anatomy and registration

  1. Brainstorm coordinate systems

  2. MRI segmentation: FreeSurfer, BrainSuite, BrainVISA, CIVET

  3. Warping default anatomy

  4. Group studies: Subjects coregistration

  5. Digitize EEG electrodes and head shape

  6. Real-time head positioning in the CTF MEG system

Graphical scripting

  1. Selecting files in the database

  2. Full analysis with one script

  3. How to write your own process

Source modeling

  1. BEM with OpenMEEG

  2. Volume source estimation

  3. Computing and displaying dipoles

  4. Beamforming methods [Under construction]

  5. Maximum Entropy on the Mean (MEM) [Under construction]

Functional connectivity

  1. Phase-amplitude coupling

Statistics

  1. Export volume source maps to SPM8 / SPM12

  2. Export surface source maps to SPM12

Other useful how-to's

  1. How to cite Brainstorm in your publications

  2. Known bugs

  3. ?MEG analysis guidelines for McGill

  4. Cleaning artifacts using SSP: examples

  5. ?Detecting bad segments in continuous recordings

  6. Detect subject movements

  7. Real-time head-tracking for adjusting head position

  8. A tutorial in Japanese (click on the menu "Brainstorm")

Examples

  1. 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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