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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 at least the first three tutorials, even if they are not illustrated with the kind of recordings of your intereset. A tutorial based on Neuromag MEG data may introduce some concepts that are useful for you, even if you only work with EEG. * If you really want a printed version of this documentation (try not to print everything): open a tutorial, go to the menu on top of each 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 == * [[Tutorials/TutBasicConcepts|Basic concepts]] * [[Tutorials/TutFirstSteps|First steps]] * [[Tutorials/TutImportAnatomy|Import individual anatomy]] * [[Tutorials/TutImportRecordings|Import recordings]] * [[Tutorials/TutExploreRecodings|Explore the recordings]] * [[Tutorials/TutHeadModel|Compute a head model]] * Sources estimation |
== 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)]] * [[Tutorials/TutFirstSteps|1. First steps]] * [[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]] * [[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]] 1. Dataset description 1. Create protocol 1. Import MRI 1. Import surfaces 1. Downsample and merge surfaces 1. Check registration with MRI 1. Fix registration with MRI 1. What happened on the hard drive * [[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]] == 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
- Dataset description
- Create protocol
- Import MRI
- Import surfaces
- Downsample and merge surfaces
- Check registration with MRI
- Fix registration with MRI
- What happened on the hard drive
?3. Importing 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
Advanced tutorials
Anatomy and registration
?Refine registration using head points
Recordings
?Review raw recordings and edit markers
Source estimation