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Differences between revisions 92 and 106 (spanning 14 versions)
⇤ ← Revision 92 as of 2011-05-14 18:54:56 →
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Editor: cpe-76-169-10-66
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← Revision 106 as of 2011-05-14 23:31:30 → ⇥
Size: 10056
Editor: cpe-76-169-10-66
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Deletions are marked like this. Additions are marked like this.
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  1. Starting Brainstorm for the first time   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Create_first_protocol|Create first protocol]]
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  1. Main interface window   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Fiducials_selection_.28MRI_Viewer.29|Fiducials selection (MRI Viewer)]]
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  1. Create first protocol   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Protocol_exploration|Protocol exploration]]
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  1. Fiducials selection (MRI Viewer)   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#MRI_visualization|MRI visualization]]
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  1. Protocol exploration   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Surfaces_visualization|Surfaces visualization]]
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  1. MRI visualization

  1. Surfaces visualization

  1. Coordinates tab		   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Coordinates_tab|Coordinates tab]]
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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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  * [[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]]
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=== Continuous Neuromag 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]][[Tutorials/SegBrainVisa|with BrainSuite]]
 1. [[Tutorials/SegBrainVisa|MRI segmentation]][[Tutorials/SegBrainVisa|with FreeSurfer]]		  1. [[Tutorials/SegBrainSuite|MRI segmentation with BrainSuite]]
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=== Recordings ===
 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]]
 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]]
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 1. [[Tutorials/TutProject|Project sources on default anatomy]]
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 1. [[Tutorials/TutClusters|Clusters of sensors]]
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 1. [[Tutorials/TutUserProcess|How to write your own processes]]

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.

  2. Then read more specific tutorials, closer to your personal interests.
  3. 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

    • Brainstorm folders

    • Brainstorm database (concept)

    • Brainstorm database (files)

  • ?1. First steps

    • Create first protocol

    • Fiducials selection (MRI Viewer)

    • Protocol exploration

    • MRI visualization

    • Surfaces visualization

    • Coordinates tab

  • ?2. Importing individual anatomy

    • Dataset description

    • Import MRI

    • Import surfaces

    • Downsample and merge surfaces

    • Check registration with MRI

    • Fix registration with MRI

    • What happened on the hard drive

  • ?3. Importing MEG 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

    • Project sources on default anatomy

  • ?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

Continuous Neuromag recordings

  1. ?Review raw recordings and edit markers

  2. Import and process raw recordings

Anatomy and registration

  1. Brainstorm coordinate systems

  2. MRI segmentation with BrainVISA

  3. MRI segmentation with BrainSuite

  4. ?Refine registration using head points

  5. Warping default anatomy

Source estimation

  1. BEM head model

  2. Volume source estimation

  3. ?Import and visualize dipoles from Neuromag Xfit

Other useful how-to's

  1. ?How to use Brainstorm without the GUI

  2. How to cite Brainstorm in your publications

  3. ?How to compile Brainstorm

  4. Known bugs

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