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| = Tutorials = == How to use those tutorials == 1. Go through all the tutorials in the section ''Getting started with Brainstorm''. In just a few hours, they will introduce you to most of the main features of the application. 1. Then read more specific tutorials, closer to your personal interests. 1. If you want a printed version of a page, click on the "print" link on the top right of the page. == Getting started with Brainstorm == |
= 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. == 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: [[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)<<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. However, note that those pages are updated with the software, and cannot be kept as long term reference documentation. * [[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. Head model]] * [[Tutorials/TutNoiseCov|6. Noise covariance]] * [[Tutorials/TutSourceEstimation|7. Source estimation]] * [[Tutorials/TutScouts|8. Scouts]] * [[Tutorials/TutProcesses|9. Scripting]] * [[Tutorials/TutStat|10. Statistics]] * [[Tutorials/TutTimefreq|11. Time-frequency]] == Advanced tutorials == === Processing continuous recordings === 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]] 1. [[Tutorials/TutMindNeuromag|Import and process raw recordings]] === Anatomy and registration === 1. [[CoordinateSystems|Brainstorm coordinate systems]] 1. [[Tutorials/LabelFreeSurfer|MRI segmentation: FreeSurfer]] 1. [[Tutorials/SegBrainVisa|MRI segmentation: BrainVISA]] 1. [[Tutorials/TutWarping|Warping default anatomy]] 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] === Source modeling === 1. [[Tutorials/TutBem|BEM with OpenMEEG]] 1. [[Tutorials/TutVolSource|Volumetric source estimation]] 1. [[Tutorials/TutXfit|Dipole models from Neuromag's Xfit]] 1. [[Tutorials/TutBEst|BrainEntropy MEM (Maximum Entropy on the Mean)]] === Other useful how-to's === 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] 1. [[Tutorials/KnownBugs|Known bugs]] == Get started (details) == |
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| * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Starting_Brainstorm_for_the_first_time|Starting Brainstorm for the first time]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Main_interface_window|Main interface window]] |
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| * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutImportAnatomy#Create_protocol|Create protocol]] | |
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| * [[Tutorials/TutImportRecordings|3. Importing recordings]] | * [[Tutorials/TutImportRecordings|3. Importing MEG recordings]] |
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| * Computing sources for a single data file * Sources visualization * Computing sources for multiple data files * Minimum norm options |
* [[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]] |
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| * Creating a scout * Scout function * Multiple scouts * Load/save scouts * Display scouts time series from the database tree * Scout toolbar and menus |
* [[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]] |
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| * Selecting files to process * Creating a pipeline * Another example: z-score and scouts |
* [[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]] |
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| * Binary processes * Mixing recordings from different runs * Tests |
* [[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]] |
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| * Introduction to complex Morlet wavelets * Edge effects * TF: Recordings * Description of the options * Display time-frequency maps * Contents of the "timefreq" files * Time and frequency bands * TF: Clusters time series * TF: Cortical sources * TF: Scouts time series * Processing time-frequency files == Advanced tutorials == === Anatomy and registration === 1. [[CoordinateSystems|Brainstorm coordinate systems]] 1. [[Tutorials/SegBrainVisa|MRI segmentation with BrainVISA]] 1. [[Tutorials/SegBrainVisa|MRI segmentation]][[Tutorials/SegBrainVisa|with BrainSuite]] 1. [[Tutorials/SegBrainVisa|MRI segmentation]][[Tutorials/SegBrainVisa|with FreeSurfer]] 1. [[Tutorials/TutRefineReg|Refine registration using head points]] 1. [[Tutorials/TutWarping|Warping default anatomy]] === Recordings === 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]] 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]] === Source estimation === 1. [[Tutorials/TutBem|BEM head model]] 1. [[Tutorials/TutVolSource|Volume source estimation]] 1. [[Tutorials/TutProject|Project sources on default anatomy]] 1. [[Tutorials/TutXfit|Import and visualize dipoles from Neuromag Xfit]] 1. [[Tutorials/TutClusters|Clusters of sensors]] === Other useful how-to's === 1. [[Tutorials/TutScript|How to use Brainstorm without the GUI]] 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] 1. [[Tutorials/TutCompile|How to compile Brainstorm]] 1. [[Tutorials/TutUserProcess|How to write your own processes]] 1. [[Tutorials/KnownBugs|Known bugs]] |
* [[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]] |
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: 978-0195307238Jean 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. However, note that those pages are updated with the software, and cannot be kept as long term reference documentation.
?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
?9. Scripting
?10. Statistics
?11. Time-frequency
Advanced tutorials
Processing continuous recordings
?Review raw recordings and edit markers
Anatomy and registration
Source modeling
?Dipole models from Neuromag's Xfit
Other useful how-to's
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
?7. Source estimation
?8. Scouts: Cortical regions of interest
?9. Processes: Graphical batching interface
?10. Statistics
?11. Time-frequency