|
Size: 10898
Comment:
|
Size: 11595
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| 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]]. <<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]]. |
| Line 86: | Line 86: |
| * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG|ECoG+sEEG epilepsy (BIDS)]] | |
| Line 102: | Line 103: |
| == Basic Electrophysiology tutorial == <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> '''Starting a new study''' * Importing RAW e-phys data '''Spike Sorting''' * Unsupervised spike-sorting * Supervised spike-sorting * Spike sorting outside of Brainstorm '''Converting Raw data to LFP''' * Without Bayesian Spike Removal * With Bayesian Spike Removal <<HTML(</TD><TD>)>> ''' e-phys functions''' * Tuning Curves * Noise Correlation * Spike Field Coherence * Raster Plots * Spike Triggered Average ''' Converting to Brainstorm events''' * Importing events from external spike-sorters <<HTML(</TD></TR></TABLE>)>> |
|
| Line 142: | Line 109: |
| * [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] | * MRI segmentation:[[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], <<BR>>[[Tutorials/SegBrainVisa|BrainVISA]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT12]], [[Tutorials/SegCIVET|CIVET]] |
| Line 147: | Line 115: |
| * [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG]] | * [[Tutorials/TutRealtime|Real-time head positioning (CTF MEG)]] * [[Tutorials/HeadMotion|Head motion detection (MEG)]] |
| Line 180: | Line 149: |
| '''Advanced processing''' * [[Tutorials/TutUserProcess|How to write your own process]] * [[Tutorials/Decoding|Decoding conditions (MVPA)]] |
'''Signal processing''' * [[Tutorials/Decoding|Machine learning: Decoding / MVPA]] |
| Line 188: | Line 156: |
| * [[Tutorials/FiberConnectivity|Virtual fibers for connectivity]] | |
| Line 189: | Line 158: |
'''Scripting''' * [[Tutorials/TutUserProcess|How to write your own process]] |
|
| Line 191: | Line 164: |
| * [[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>)>> * [[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]] |
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] [TODO] 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!