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| == 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. |
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. == How to use the tutorial pages == 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. |
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| * [[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]] == Advanced tutorials == === Continuous Neuromag 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/SegBrainVisa|MRI segmentation with BrainVISA]] 1. [[Tutorials/SegBrainSuite|MRI segmentation with BrainSuite]] 1. [[Tutorials/TutWarping|Warping default anatomy]] === Source estimation === 1. [[Tutorials/TutBem|BEM head model]] 1. [[Tutorials/TutVolSource|Volume source estimation]] 1. [[Tutorials/TutXfit|Import and visualize dipoles from Neuromag Xfit]] 1. [[Tutorials/TutMem|BrainEntropy MEM (Maximum Entropy on the Mean)]] === Other useful how-to's === 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] 1. [[Tutorials/TutScript|How to use Brainstorm without the GUI]] 1. [[Tutorials/TutCompile|How to compile Brainstorm]] 1. [[Tutorials/KnownBugs|Known bugs]] == Getting 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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| 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]] |
* [[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]] |
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| * [[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]] |
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| * [[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]] |
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| * [[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]] |
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| * [[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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| * [[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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| * [[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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| * [[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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== 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]] |
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 a editor of this wiki. Please email us if you would like to contribute.
How to use the tutorial pages
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.
Read more specific tutorials (see Advanced Tutorials below), related to your personal interests/needs.
- If you need a printed version of a page, click on the "print" link at the top-right corner of the page.
Getting started with Brainstorm
?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
Advanced tutorials
Continuous Neuromag recordings
?Review raw recordings and edit markers
Anatomy and registration
Source estimation
Other useful how-to's
Getting 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