= 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.
 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.

== 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]]
  * [[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]]
  * [[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]]
 * [[Tutorials/TutExploreRecodings|4. Exploring the recordings]]
  * [[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]]
 * [[Tutorials/TutHeadModel|5. Computing a head model]]
  * [[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]]
 * [[Tutorials/TutNoiseCov|6. Computing a noise covariance matrix]]
  * [[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]]
 * [[Tutorials/TutSourceEstimation|7. Source estimation]]
  * [[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]]
 * [[Tutorials/TutScouts|8. Scouts: Cortical regions of interest]]
  * [[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]]
 * [[Tutorials/TutProcesses|9. Processes: Graphical batching interface]]
  * [[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]]
 * [[Tutorials/TutStat|10. Statistics]]
  * [[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]]
 * [[Tutorials/TutTimefreq|11. Time-frequency]]
  * [[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]]

== 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]]