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| == Important notes == * In all the tutorials, we will consider that you are working with the source distribution of Brainstorm, as it is the recommanded way to use this toolbox. * If you are working with compiled binaries, some menus might be missing, but everything else should work the same way. * Before starting using Brainstorm with your own data, you should go through __all __the tutorials. * 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, * Click on the ''Back ''button of your browser, and go to next tutorial. |
== 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. |
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| == Starting with Brainstorm == Intro: [[BstFolders|Introduction to Brainstorm structure]] |
== Getting started with Brainstorm == * [[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)]] |
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| 1. [[Tutorials/TutFirstSteps|First steps]] 1. [[Tutorials/TutImportAnatomy|Importing individual anatomy]] 1. [[Tutorials/TutImportRecordings|Importing recordings]] 1. [[Tutorials/TutExploreRecodings|Exploring the recordings]] 1. [[Tutorials/TutHeadModel|Computing a head model]] 1. [[Tutorials/TutNoiseCov|Computing a noise covariance matrix]] 1. [[Tutorials/TutSourceEstimation|Source estimation]] 1. [[Tutorials/TutScouts|Scouts: cortical regions of interest]] 1. [[Tutorials/TutProcesses|Processes: Graphical batching interface]] |
* [[Tutorials/TutFirstSteps|1. First steps]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Starting_Brainstorm_for_the_first_time|Starting Brainstorm for the first time]] |
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| == Other useful tutorials == 1. [[CiteBrainstorm|Cite Brainstorm in your publications]] |
* [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Main_interface_window|Main interface window]] * [[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#Create_protocol|Create protocol]] * [[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 recordings]] * Import recordings * Channel file * MEG recordings * Managing conditions * [[Tutorials/TutExploreRecodings|4. Exploring the recordings]] * Display recordings * Time exploration * Sensors selection * Time series in columns * Time selection * Good / bad channels * Colormap configuration * Toolbar / Manipulating multiple windows * Database navigator * Snapshots * Keyboard shortcuts * [[Tutorials/TutHeadModel|5. Computing a head model]] * Forward problem * Single sphere model * Overlapping spheres model * Selection of a head model * Batching head model computation * [[Tutorials/TutNoiseCov|6. Computing a noise covariance matrix]] * Compute from recordings * Noise covariance from another dataset * [[Tutorials/TutSourceEstimation|7. Source estimation]] * Computing sources for a single data file * Sources visualization * Computing sources for multiple data files * Minimum norm options * [[Tutorials/TutScouts|8. Scouts: Cortical regions of interest]] * Creating a scout * Scout function * Multiple scouts * Load/save scouts * Display scouts time series from the database tree * Scout toolbar and menus * [[Tutorials/TutProcesses|9. Processes: Graphical batching interface]] * Selecting files to process * Creating a pipeline * Another example: z-score and scouts * [[Tutorials/TutStat|10. Statistics]] * Binary processes * Mixing recordings from different runs * Tests * [[Tutorials/TutTimefreq|11. Time-frequency]] * 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]] |
Tutorials
How to use those tutorials
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.
- Then read more specific tutorials, closer to your personal interests.
- 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
?0. Brainstorm architecture
?1. First steps
?2. Importing individual anatomy
?3. Importing recordings
- Import recordings
- Channel file
- MEG recordings
- Managing conditions
?4. Exploring the recordings
- Display recordings
- Time exploration
- Sensors selection
- Time series in columns
- Time selection
- Good / bad channels
- Colormap configuration
- Toolbar / Manipulating multiple windows
- Database navigator
- Snapshots
- Keyboard shortcuts
?5. Computing a head model
- Forward problem
- Single sphere model
- Overlapping spheres model
- Selection of a head model
- Batching head model computation
?6. Computing a noise covariance matrix
- Compute from recordings
- Noise covariance from another dataset
?7. Source estimation
- Computing sources for a single data file
- Sources visualization
- Computing sources for multiple data files
- Minimum norm options
?8. Scouts: Cortical regions of interest
- Creating a scout
- Scout function
- Multiple scouts
- Load/save scouts
- Display scouts time series from the database tree
- Scout toolbar and menus
?9. Processes: Graphical batching interface
- Selecting files to process
- Creating a pipeline
- Another example: z-score and scouts
?10. Statistics
- Binary processes
- Mixing recordings from different runs
- Tests
?11. Time-frequency
- 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
?Refine registration using head points
Recordings
?Review raw recordings and edit markers
Source estimation