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= 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 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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== Required background == | |
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* 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: |
* 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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. * 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. |
* 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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---- /!\ '''Edit conflict - other version:''' |
* Reference book: [[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: Peter Hansen, Morten Kringelbach, Riitta Salmelin<<BR>> ''Oxford University Press'', 2010, 448 pages |
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---- . * A draft version of the chapter can be found [[attachment:Baillet_MEG Draft.pdf|here]]. |
* Reference book: [[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: Jean Decety, John T. Cacioppo<<BR>>''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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Now you are well equipped to go through the software tutorial. Enjoy! | * 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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---- /!\ '''Edit conflict - your version:''' |
Now you are well equipped to go through the software tutorial, '' Enjoy! '' |
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---- . * A draft version of the chapter can be found [[attachment:Baillet_MEG Draft.pdf|here]]. |
== 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. |
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Now you are well equipped to go through the software tutorial. Enjoy! | 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. |
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---- /!\ '''End of edit conflict''' |
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. |
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---- | === 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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== 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 == * [[Tutorials/BstFolders|0. Brainstorm architecture]] * [[Tutorials/TutFirstSteps|1. First steps]] * [[Tutorials/TutImportAnatomy|2. Importing individual anatomy]] * [[Tutorials/TutImportRecordings|3. Importing MEG 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]] |
=== 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]] 1. [[Tutorials/TutMindNeuromag|Import and process raw recordings]] |
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1. [[Tutorials/SegBrainVisa|MRI segmentation with BrainVISA]] 1. [[Tutorials/SegBrainSuite|MRI segmentation with BrainSuite]] |
1. [[Tutorials/LabelFreeSurfer|MRI segmentation: FreeSurfer]] 1. [[Tutorials/SegBrainVisa|MRI segmentation: BrainVISA]] 1. [[Tutorials/SegBrainSuite|MRI segmentation: BrainSuite]] |
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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]] |
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1. [[Tutorials/TutBem|Boundary Element Modeling (BEM)]] 1. [[Tutorials/TutVolSource|Source estimation not constrained to cortical surface]] 1. [[Tutorials/TutXfit|Import and visualize dipole models from another software (Neuromag's Xfit]]) 1. [[Tutorials/TutMem|BrainEntropy MEM (Maximum Entropy on the Mean)]] |
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] |
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1. [[Tutorials/TutScript|How to use Brainstorm without the GUI]] 1. [[Tutorials/TutCompile|How to compile Brainstorm]] |
1. [[CoordinateSystems|Coordinate systems]] |
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== Getting started (details) == * [[Tutorials/BstFolders|0. Brainstorm architecture]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/BstFolders#Brainstorm_folders|Brainstorm folders]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/BstFolders#Brainstorm_database_.28concept.29|Brainstorm database (concept)]] * [[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 |
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.orgReference book: MEG: An Introduction to Methods
Editors: Peter Hansen, Morten Kringelbach, Riitta Salmelin
Oxford University Press, 2010, 448 pagesReference book: The Oxford Handbook of Social Neuroscience
Editors: Jean Decety, John T. Cacioppo
Oxford University Press, 2011, 1128 pages
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
Source modeling
?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