|
Size: 11321
Comment:
|
Size: 12578
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| 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]]. |
| Line 5: | Line 5: |
| 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]]. |
| Line 11: | Line 11: |
| <<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>)>> |
| Line 19: | Line 19: |
| <<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>)>> |
| Line 29: | Line 29: |
| <<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>)>> |
| Line 47: | Line 47: |
| <<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>)>> |
| Line 59: | Line 59: |
| <<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>)>> |
| Line 85: | Line 85: |
| * [[Tutorials/Epileptogenicity|SEEG epileptogenicity maps]] | * Intracranial EEG: iEEG/[[Tutorials/Epileptogenicity|SEEG epileptogenicity maps]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG|ECoG+sEEG epilepsy (BIDS)]] |
| Line 94: | Line 95: |
| * [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence|MEG corticomuscular coherence (CTF)]] | |
| Line 98: | Line 100: |
| * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] ''' [TODO]''' | * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] |
| Line 108: | Line 110: |
| * [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] | * 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]] |
| Line 119: | Line 122: |
| * [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Artifact_cleaning_with_ICA|ICA analysis]] | |
| Line 123: | Line 127: |
| '''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]] |
|
| Line 125: | Line 136: |
| * [[CiteBrainstorm|How to cite Brainstorm]] [TODO] | * [[Tutorials/Plugins|Plugins]] * [[MnePython|MNE-Python]] * [[CiteBrainstorm|How to cite Brainstorm]] |
| Line 129: | Line 142: |
| '''Deprecated documentation''' * [[Tutorials/VisualSingleOrig|MEG visual: single subject (Elekta/Orig)]] * [[Tutorials/VisualGroupOrig|MEG visual: group study (Elekta/Orig)]] |
|
| Line 139: | Line 146: |
| * [[Tutorials/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] |
|
| Line 140: | Line 151: |
| * [[Tutorials/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] |
|
| Line 146: | Line 155: |
'''Advanced processing''' * [[Tutorials/TutUserProcess|How to write your own process]] * [[Tutorials/Decoding|Decoding conditions (MVPA)]] |
* [[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/FemMedianNerveCharm|FEM median nerve example]] '''Signal processing''' * [[Tutorials/Decoding|Machine learning: Decoding / MVPA]] |
| Line 154: | Line 171: |
| * [[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/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>)>> == Single/Multi-Unit Electrophysiology == Learn how to use Brainstorm for analyzing single/multi-unit electrophysiological data in a variety of preparations: |
| Line 169: | Line 195: |
| * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting#Supervised_Spike_Sorting|Spike-sorting]] | * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting|Spike-sorting]] |
| Line 177: | Line 203: |
| * [[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]] |
| Line 188: | Line 214: |
| * [[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) |
| Line 197: | Line 224: |
| * [[https://mitpress.mit.edu/books/matlab-brain-and-cognitive-scientists|MATLAB for Brain and Cognitive Scientists]], Mike X Cohen, MIT press, 2017 |
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.
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 |
Other analysis scenarios
Advanced tutorials
| Anatomy and registration
Recordings Scripting Software | Source modeling Finite Element Modeling Signal processing Connectivity |
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.
MATLAB for Brain and Cognitive Scientists, Mike X Cohen, MIT press, 2017
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!