Brainstorm
  • Comments
  • Menu
    • Attachments
    • Versions
    • Raw Text
    • Print View
  • Login

Software

  • Introduction

  • Gallery

  • Download

  • Installation

Users

  • Tutorials

  • Forum

  • Courses

  • Community

  • Publications

Development

  • What's new

  • What's next

  • About us

  • Contact us

  • Contribute

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
Differences between revisions 90 and 108 (spanning 18 versions)
⇤ ← Revision 90 as of 2011-05-14 18:52:08 →
Size: 3292
Editor: cpe-76-169-10-66
Comment:
← Revision 108 as of 2011-05-15 06:25:24 → ⇥
Size: 9986
Editor: cpe-76-169-10-66
Comment:
Deletions are marked like this. Additions are marked like this.
Line 9: Line 9:
 [[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)]]		   * [[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)]]
Line 14: Line 14:
  * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Create_first_protocol|Create first protocol]]
Line 15: Line 16:
  1. Starting Brainstorm for the first time   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Fiducials_selection_.28MRI_Viewer.29|Fiducials selection (MRI Viewer)]]
Line 17: Line 18:
  1. Main interface window   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Protocol_exploration|Protocol exploration]]
Line 19: Line 20:
  1. Create first protocol   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#MRI_visualization|MRI visualization]]
Line 21: Line 22:
  1. Fiducials selection (MRI Viewer)   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Surfaces_visualization|Surfaces visualization]]
Line 23: Line 24:
  1. Protocol exploration

  1. MRI visualization

  1. Surfaces visualization

  1. Coordinates tab		   * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Coordinates_tab|Coordinates tab]]
Line 31: Line 26:
  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]]
Line 41: Line 39:
  * [[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]]
Line 42: Line 51:
  * [[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]]
Line 43: Line 57:
  * [[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]]
Line 44: Line 60:
  * [[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]]
Line 45: Line 66:
  * [[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]]
Line 46: Line 73:
  * [[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]]
Line 47: Line 77:
  * [[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]]
Line 48: Line 81:
  * [[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]]
Line 50: Line 94:
=== Continuous Neuromag recordings ===
 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]]
 1. [[Tutorials/TutMindNeuromag|Import and process raw recordings]]
Line 53: Line 101:
 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/SegBrainSuite|MRI segmentation with BrainSuite]]
Line 57: Line 103:

=== Recordings ===
 1. [[Tutorials/TutRawViewer|Review raw recordings and edit markers]]
 1. [[Tutorials/TutMindNeuromag|Neuromag raw recordings]]
Line 65: Line 107:
 1. [[Tutorials/TutProject|Project sources on default anatomy]]
Line 67: Line 108:
 1. [[Tutorials/TutClusters|Clusters of sensors]]
Line 70: Line 110:
 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]]
Line 71: Line 112:
 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]]
Line 73: Line 113:
 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. 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 cite Brainstorm in your publications

  2. ?How to use Brainstorm without the GUI

  3. ?How to compile Brainstorm

  4. Known bugs

  • MoinMoin Powered
  • Python Powered
  • GPL licensed
  • Valid HTML 4.01