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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]]. <<BR>>Some sections are still being edited or under review: [[Tutorials/Review|Editing process]]. | 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]]. |
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| <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> '''[TODO]''' | <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> |
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| * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG|ECoG+sEEG epilepsy (BIDS)]] | |
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| * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] ''' [TODO]''' | * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] |
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| * [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] | * MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], <<BR>>[[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT12]], [[Tutorials/SegCIVET|CIVET]] |
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| * [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG]] | * [[Tutorials/TutRealtime|Real-time head positioning (CTF MEG)]] * [[Tutorials/HeadMotion|Head motion detection (MEG)]] |
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| * [[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]] | * Realistic head model: <<BR>>[[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]]<<BR>>[[https:///Duneuro|Realistic head model: FEM with DUNEuro]] |
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| '''Advanced processing''' * [[Tutorials/TutUserProcess|How to write your own process]] * [[Tutorials/Decoding|Decoding conditions (MVPA)]] |
'''Signal processing''' * [[Tutorials/Decoding|Machine learning: Decoding / MVPA]] |
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| * [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] | * [[Tutorials/FiberConnectivity|Virtual fibers for connectivity]] * [[MnePython|Using MNE-Python from Brainstorm]] * [[Tutorials/EZFingerprint|Epileptogenic Zone Fingerprint]] '''Scripting''' * [[Tutorials/TutUserProcess|How to write your own process]] |
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| * [[ExportBids|Export MEG data files to BIDS format]] <<HTML(</TD></TR></TABLE>)>> == Basic electrophysiology tutorial (single & multiunit activity): == <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> '''Starting a new study''' * [[https://neuroimage.usc.edu/brainstorm/e-phys/Introduction|Importing RAW e-Phys data]] '''Spike Sorting''' * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting|Unsupervised spike-sorting]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting#Supervised_Spike_Sorting|Supervised spike-sorting]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting#Spike_sorting_outside_of_Brainstorm|Spike sorting outside of Brainstorm]] '''Converting Raw data to LFP''' * [[https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP|Without Bayesian Spike Removal]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP#Conversion_to_LFP_with_Bayesian_Spike_Removal|With Bayesian Spike Removal]] <<HTML(</TD><TD>)>> ''' e-Phys functions''' |
* [[ExportBids|Export raw data to BIDS format]] <<HTML(</TD></TR></TABLE>)>> == Invasive neurophysiology == Learn how to use Brainstorm for studying single & multiunit activity. <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> * [[https://neuroimage.usc.edu/brainstorm/e-phys/Introduction|Importing raw e-phys data]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting#Supervised_Spike_Sorting|Spike-sorting]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents|Using external spike-sorters]] * [[https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP|Converting raw data to LFP]] <<HTML(</TD><TD>)>> |
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| ''' Converting to Brainstorm events''' * [[https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents|Importing events from external spike-sorters]] |
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 the old 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. The number between brackets represents the number of printed pages for each tutorial. All in one page.
| Starting a new study 1. Create a new protocol [9] 2. Import the subject anatomy [8] 3. Explore the anatomy [13] Reviewing 4. Channel file / MRI registration [11] 5. Continuous recordings [9] 6. Multiple windows [5] 7. Event markers [10] Pre-processing 8. Stimulation delays [9] 9. Select files / Run processes [11] 10. Power spectrum / Frequency filters [15] 11. Bad channels [6] 12. Artifact detection [8] 13. Artifact cleaning with SSP [16] 14. Additional bad segments [7] | Epoching and averaging 15. Import epochs [9] 16. Average response [7] 17. Visual exploration [10] 18. Colormaps [5] 19. Clusters of sensors [4] Source modeling 20. Head model [9] 21. Noise/data covariance [7] 22. Source estimation [28] 23. Scouts [17] Advanced processing 24. Time-frequency [33] 25. Difference [13] 26. Statistics [30] 27. Workflows [10] 28. Scripting [31] |
Other analysis scenarios
Advanced tutorials
| Anatomy and registration
Recordings Software Deprecated documentation | Source modeling
Signal processing
Scripting |
Invasive neurophysiology
Learn how to use Brainstorm for studying single & multiunit activity.
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:
Nature Neuroscience review paper on MEG for Human Electrophysiology and Imaging (Baillet S, 2017)
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!