Differences between revisions 355 and 362 (spanning 7 versions)

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

1. Create a new protocol

2. Import the subject anatomy

3. Explore the anatomy

Reviewing

4. Channel file / MRI registration

5. Continuous recordings

6. Multiple windows

7. Event markers

Pre-processing

8. Stimulation delays

9. Select files / Run processes

10. Power spectrum / Frequency filters

11. Bad channels

12. Artifact detection

13. Artifact cleaning with SSP

14. Additional bad segments

Epoching and averaging

15. Import epochs

16. Average response

17. Visual exploration

18. Colormaps

19. Clusters of sensors

Source modeling

20. Head model

21. Noise/data covariance

22. Source estimation

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 electrophysiology

Learn how to use Brainstorm for analyzing single/multi-unit electrophysiological data in a variety of preparations:

Background readings

These 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:

MEG for Human Electrophysiology and Imaging (Baillet S, Nature Neuroscience, 2017)
Connectomics of Human Electrophysiology (Sadaghiani S, Brookes M, Baillet S, Neuroimage, 2022)
Introduction to MEG (Medical College of Wisconsin)
A non-technical overview of MEG and EEG, with an emphasis on source modeling.
MEG: An Introduction to Methods
Editors: P Hansen, M Kringelbach, R Salmelin, Oxford University Press, 2010, 448 pages.
The Oxford Handbook of Social Neuroscience
Editors: J Decety, JT Cacioppo, Oxford University Press, 2011, 1128 pages
A draft version of the MEG chapter by Sylvain Baillet can be found here.
Good practice for conducting and reporting MEG research, Gross et al, Neuroimage, 2013.
Slides from a selection of educational courses: megcommunity.org
We can also come and organize a training session at your institution, or visit us at the MNI.

Now you are well equipped to go through the software tutorial, Enjoy!

Tutorials (last edited 2024-06-03 14:53:21 by RaymundoCassani)

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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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-'''Advanced processing'''
+'''Advanced processes'''
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+<<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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+Line 186:
-<<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]]

<<HTML(</TD></TR></TABLE>)>>

== Multiunit electrophysiology ==
Learn how to use Brainstorm for studying single & multiunit activity.
+== Single/multi-unit electrophysiology ==
Learn how to use Brainstorm for analyzing single/multi-unit electrophysiological data in a variety of preparations:
-Line 203:
+Line 201:
- * [[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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+Line 212:
- * [[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)

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