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| == Important notes == * Distribution: * 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 __all__'''__ the tutorials__''' in the following section: "''Getting started with Brainstorm''". In just a few hours, they will introduce you to most of the main features of the application. * Then you can read more specific tutorials, closer to your personal interests. * If you want a printed version of this documentation: * Open a tutorial, go to the menu on top of the 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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| === Dataset description === The dataset that will be used for tutorials #2 to #10 is a somatotopy experiment recorded with a CTF 151 MEG system. |
* [[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)]] |
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| Please download bst_sample_ctf.zip from the [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] section. Unzip it in a folder you will dedicate to original data. It can be anywhere but __not__ in the Brainstorm database or program folder. Example: | * [[Tutorials/TutFirstSteps|1. First steps]] |
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| * __Windows__: My documents\MEG\sample_ctf\ * __Linux__: /home/username/MEG/sample_ctf/ * __MacOS__: Documents/MEG/sample_ctf/ |
* [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Create_first_protocol|Create first protocol]] |
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| ||<width="150px" style="vertical-align: top;">File: ||'''bst_sample_ctf.zip''' || ||<style="vertical-align: top;">Acquisition system: ||CTF MEG, 151 axial gradiometers, La Salpetriere Hospital, Paris || ||<style="vertical-align: top;">Protocol: ||Shuffled electrical stimulations of the thumb fingers from both hands. The idea is to get a map of the primary sensory response on the cortex || ||<style="vertical-align: top;">Author: ||Data provided courtesy of Sabine Meunier || ||<style="vertical-align: top;">Anatomy directory: ||- T1-MRI of the subject in CTF format (.mri).<<BR>>- Cortex and head surfaces extracted with BrainVISA software([[Tutorials/SegBrainVisa|see tutorial]]) || ||<style="vertical-align: top;">Datasets directory: ||- somMGYO-18av.ds: average response for the stimulation of the right thumb (one subject, 400 trials) .<<BR>>- somMDYO-18av.ds: average response for the stimulation of the left thumb (one subject, 400 trials) || ||<style="vertical-align: top;">Observations: ||Stimulus occurs at time 0. There's a first tiny wave occuring at about 20ms or so but it's not too clear on all fingers. So if you are to compute cortical maps, start by the 40ms peak which is also of interest and which has much better SNR. || |
* [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Fiducials_selection_.28MRI_Viewer.29|Fiducials selection (MRI Viewer)]] |
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| * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutFirstSteps#Protocol_exploration|Protocol exploration]] | |
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| === Step by step tutorials === * [[Tutorials/BstFolders|0. Introduction to Brainstorm structure]] * [[Tutorials/TutFirstSteps|1. First steps]] |
* [[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]] |
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| * [[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]] |
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| * [[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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| * [[Tutorials/TutScouts|8. Scouts: cortical regions of interest]] | * [[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]] |
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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]] * [[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]] |
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| == Other useful tutorials == 1. [[Tutorials/SegBrainVisa|Extract head and cortex surface with BrainVISA]] 1. [[Tutorials/SegBrainSuite|Extract head and cortex surface with BrainSuite]] 1. [[Tutorials/SegFreeSurfer|Extract head and cortex surface with FreeSurfer]] 1. [[Tutorials/TutInverseExpertMode|More inverse methods]] 1. [[CiteBrainstorm|Cite Brainstorm in your publications]] |
== 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
?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