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| These tutorial pages suppose you are comfortable with the basic concepts of MEG/EEG analysis and source imaging. If you're not, we encourage you to read some [[http://neuroimage.usc.edu/brainstorm/Tutorials#Background_readings|background literature]].<<BR>>To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]].<<BR>><<HTML(<FONT color="#C0C0C0" >)>>If you are looking for the old tutorials, they are still available [[TutorialsOld|here]]. <<HTML(</FONT>)>> | These tutorial pages suppose you are comfortable with the basic concepts of MEG/EEG analysis and source imaging. If you're not, we encourage you to read some [[http://neuroimage.usc.edu/brainstorm/Tutorials#Background_readings|background literature]].<<BR>>To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]].<<BR>><<HTML(<FONT color="#C0C0C0" >)>>If you are looking for former versions of the tutorials, they are still available [[TutorialsOld|here]]. <<HTML(</FONT>)>> |
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| The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. The number between brackets represents the number of printed pages for each tutorial. All in [[Tutorials/AllIntroduction|one page]]. | The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. They can be separately consulted (links below), or all in [[Tutorials/AllIntroduction|one page]]. |
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| <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> |
<<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> |
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| <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
<<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> |
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| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[15] <<HTML(</FONT>)>> <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <<HTML(<FONT color="#DDDDDD">)>>[16] <<HTML(</FONT>)>> <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
<<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> |
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| <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> |
<<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> |
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| <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> '''[TODO]''' <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>>[17] <<HTML(</FONT>)>> '''Advanced processing''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[33] <<HTML(</FONT>)>> <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>>[30] <<HTML(</FONT>)>> <<HTML( )>>27. [[Tutorials/Workflows|Workflows]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>28. [[Tutorials/Scripting|Scripting]] <<HTML(<FONT color="#DDDDDD">)>>[31] <<HTML(</FONT>)>> |
<<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> '''Advanced processes''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>27. [[Tutorials/Workflows|Workflows]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML( )>>28. [[Tutorials/Scripting|Scripting]] <<HTML(<FONT color="#DDDDDD">)>> <<HTML(</FONT>)>> <<HTML(</TD></TR></TABLE>)>> == Advanced tutorials == <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> '''Anatomy and registration''' * [[CoordinateSystems|Brainstorm coordinate systems]] * MRI segmentation: [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT12]], [[Tutorials/LabelFreeSurfer|FreeSurfer]], <<BR>>[[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegFastSurfer|FastSurfer]], [[Tutorials/SegCIVET|CIVET]] * [[Tutorials/DefaultAnatomy|Using the anatomy templates]] * [[Tutorials/TutWarping|Warping the anatomy templates]] * [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] * [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] * [[Tutorials/TutRealtime|Real-time head positioning (CTF MEG)]] * [[Tutorials/HeadMotion|Head motion detection (MEG)]] '''Recordings''' * [[Tutorials/MontageEditor|Montage editor]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Artifact_cleaning_with_ICA|ICA analysis]] * [[Tutorials/SSPCookbook|SSP cookbook]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] * [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] '''Scripting''' * [[Tutorials/TutUserProcess|How to write your own process]] * [[ExportSpm8|Export volume sources to SPM8/SPM12]] * [[ExportSpm12|Export surface sources to SPM12]] * [[ExportBids|Export raw data to BIDS format]] '''Software''' * [[Tutorials/Plugins|Plugins]] * [[MnePython|MNE-Python]] * [[CiteBrainstorm|How to cite Brainstorm]] * [[Tutorials/KnownBugs|Known bugs]] * [[Tutorials/Plotly|Export figures to Plotly]] <<HTML(</TD><TD>)>> '''Source modeling''' * [[Tutorials/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] * [[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]] * [[Tutorials/TutDipScan|Dipoles: Scanning and displaying]] * [[Tutorials/DipoleFitting|Dipoles: FieldTrip dipole fitting]] * [[Tutorials/TutBEst|Maximum entropy on the mean (MEM)]] * [[Tutorials/Beamformers|Other beamforming methods]] * [[Tutorials/Simulations|Simulations]] '''Finite Element Modeling''' * [[Tutorials/Duneuro|Realistic head model: FEM with DUNEuro]] * [[Tutorials/FemMesh|FEM mesh generation]] * [[Tutorials/FemTensors|FEM tensors estimation]] * [[Tutorials/FemMedianNerve|FEM median nerve example]] '''Signal processing''' * [[Tutorials/Decoding|Machine learning: Decoding / MVPA]] * [[Tutorials/TutPac|Phase-amplitude coupling: Method]] * [[Tutorials/Resting|Phase-amplitude coupling: Example]] * [[Tutorials/PLS|Partial Least Squares (PLS)]] * [[Tutorials/EZFingerprint|Epileptogenic Zone Fingerprint]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof|FOOOF: Fitting Oscillations & One-Over-F]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT|SPRiNT: Spectral Param. Resolved in Time]] '''Connectivity''' * [[Tutorials/Connectivity|Functional connectivity]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence|Corticomuscular coherence]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph|Connectivity graphs]] * [[Tutorials/FiberConnectivity|Virtual fibers for connectivity]] * [[https://neuroimage.usc.edu/brainstorm/GrangerCausality|Granger causality]] |
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| * [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence|MEG corticomuscular coherence (CTF)]] | |
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| * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] ''' [TODO]''' <<HTML(</TD></TR></TABLE>)>> == Advanced tutorials == <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> '''Anatomy and registration''' * [[CoordinateSystems|Brainstorm coordinate systems]] * [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] * [[Tutorials/DefaultAnatomy|Using the anatomy templates]] * [[Tutorials/TutWarping|Warping the anatomy templates]] * [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] * [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] * [[Tutorials/TutRealtime|Real-time head positioning (CTF MEG)]] * [[Tutorials/HeadMotion|Head motion detection (MEG)]] '''Recordings''' * [[Tutorials/MontageEditor|Montage editor]] * [[Tutorials/SSPCookbook|SSP cookbook]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] * [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] '''Software''' * [[CiteBrainstorm|How to cite Brainstorm]] [TODO] * [[Tutorials/KnownBugs|Known bugs]] * [[Tutorials/Plotly|Export figures to Plotly]] '''Deprecated documentation''' * [[Tutorials/VisualSingleOrig|MEG visual: single subject (Elekta/Orig)]] * [[Tutorials/VisualGroupOrig|MEG visual: group study (Elekta/Orig)]] <<HTML(</TD><TD>)>> '''Source modeling''' * [[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]] * [[Tutorials/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] * [[Tutorials/TutDipScan|Dipoles: Scanning and displaying]] * [[Tutorials/DipoleFitting|Dipoles: FieldTrip dipole fitting]] * [[Tutorials/TutBEst|Maximum entropy on the mean (MEM)]] * [[Tutorials/Beamformers|Other beamforming methods]] '''Advanced processing''' * [[Tutorials/TutUserProcess|How to write your own process]] * [[Tutorials/Decoding|Decoding conditions (MVPA)]] * [[Tutorials/TutPac|Phase-amplitude coupling: Method]] * [[Tutorials/Resting|Phase-amplitude coupling: Example]] * [[Tutorials/PLS|Partial Least Squares (PLS)]] * [[Tutorials/Connectivity|Functional connectivity]] [TODO] * [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] * [[ExportSpm8|Export volume sources to SPM8/SPM12]] * [[ExportSpm12|Export surface sources to SPM12]] * [[ExportBids|Export raw data to BIDS format]] <<HTML(</TD></TR></TABLE>)>> == Invasive neurophysiology == Learn how to use Brainstorm for studying single & multiunit activity. |
* [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] == Single/multi-unit electrophysiology == Learn how to use Brainstorm for analyzing single/multi-unit electrophysiological data in a variety of preparations: |
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| * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting#Supervised_Spike_Sorting|Spike-sorting]] | * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting|Spike-sorting]] |
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| * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions|Tuning Curves]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Noise_Correlation|Noise Correlation]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Spike_Field_Coherence|Spike Field Coherence]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Raster_Plots|Raster Plots]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Spike_triggered_Average|Spike Triggered Average]] |
* [[https://neuroimage.usc.edu/brainstorm/e-phys/functions|Tuning curves]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Noise_correlation|Noise correlation]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Spike_field_coherence|Spike field coherence]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Raster_plots|Raster plots]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/functions#Spike_triggered_average|Spike triggered average]] |
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| * [[http://rdcu.be/pydB|Nature Neuroscience review paper on MEG for Human Electrophysiology and Imaging]] (Baillet S, 2017) | * [[http://rdcu.be/pydB|MEG for Human Electrophysiology and Imaging]] (Baillet S, Nature Neuroscience, 2017) * [[https://doi.org/10.1016/j.neuroimage.2021.118788|Connectomics of Human Electrophysiology]] (Sadaghiani S, Brookes M, Baillet S, Neuroimage, 2022) |
Tutorials
These tutorial pages suppose you are comfortable with the basic concepts of MEG/EEG analysis and source imaging. If you're not, we encourage you to read some background literature.
To get a quick overview of the software interface, you can watch this introduction video.
If you are looking for former versions of the tutorials, they are still available ?here.
Get started
The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. They can be separately consulted (links below), or all in one page.
| Starting a new study Reviewing 4. Channel file / MRI registration Pre-processing 9. Select files / Run processes 10. Power spectrum / Frequency filters 11. Bad channels | Epoching and averaging 15. Import epochs 16. Average response 18. Colormaps Source modeling 20. Head model 23. Scouts Advanced processes 24. Time-frequency 25. Difference 26. Statistics 27. Workflows 28. Scripting |
Advanced tutorials
| Anatomy and registration
Recordings Scripting Software | Source modeling Finite Element Modeling Signal processing Connectivity |
Other analysis scenarios
|
Single/multi-unit electrophysiologyLearn how to use Brainstorm for analyzing single/multi-unit electrophysiological data in a variety of preparations:
Background readingsThese tutorial pages suppose you are comfortable with the basic concepts of MEG and EEG source imaging. If you're not, we encourage you to read some background information, which will quickly help you getting up to speed with this field:
Now you are well equipped to go through the software tutorial, Enjoy!
Tutorials (last edited 2024-06-03 14:53:21 by RaymundoCassani) |