|
Size: 9380
Comment:
|
Size: 11820
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| '''[UNDER CONSTRUCTION]''' 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/TutorialsNew#Background_readings|background literature]].<<BR>>To get a quick overview of the software interface, you can watch this [[Screenshots|introduction video]]. |
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>)>> |
| Line 7: | Line 5: |
| The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. In just a few hours, you will be introduced to the essential features of the application. The number between brackets represents the number of printed pages for each tutorial. <<HTML(<TABLE class="tuto-table"><TR><TD>)>> |
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]]. <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> |
| Line 17: | Line 15: |
| <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> | <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> |
| Line 23: | Line 21: |
| <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[] <<HTML(</FONT>)>> | <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 31: | Line 29: |
| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
<<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>)>> |
| Line 39: | Line 37: |
| <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> | <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
| Line 45: | Line 43: |
| '''Epoching and averaging''''''<<BR>>[Under construction] ''' <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML( )>>16. [[Tutorials/Averaging|Average response]] [Under construction] <<HTML( )>>17. [[Tutorials/ExploreRecordings|Exploring the average response]] <<HTML( )>>18. 2D/3D topography <<HTML( )>>19. [[Tutorials/Colormaps|Colormaps]] <<HTML( )>>?? Clusters of sensors <<HTML(</TD><TD>)>> '''Source modeling''''''<<BR>>[Under construction] ''' <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise covariance]] <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] '''Advanced signal processing''''''<<BR>>[Under construction] ''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] <<HTML( )>>27. Phase-amplitude coupling '''Scripting'''''' <<BR>>[Under construction] ''' <<HTML( )>>28. [[Tutorials/Scripting|Complete tutorial script]] <<HTML( )>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]] |
<<HTML(</TD><TD>)>> '''Epoching and averaging''' <<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>)>> '''Source modeling''' <<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>)>> <<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>)>> |
| Line 90: | Line 82: |
| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG and epilepsy]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory|MEG auditory tutorial (CTF)]] 1. [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] [Under construction] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa|MEG median nerve (Yokogawa/KIT)]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag|MEG median nerve (Elekta-Neuromag)]] [Under construction] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Resting|MEG resting state (CTF)]] |
<<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> * [[Tutorials/Epilepsy|EEG and epilepsy]] * [[Tutorials/Epileptogenicity|SEEG epileptogenicity maps]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG|ECoG+sEEG epilepsy (BIDS)]] * [[Tutorials/VisualSingle|MEG visual: single subject (Elekta/BIDS)]] * [[Tutorials/VisualGroup|MEG visual: group study (Elekta/BIDS)]] * [[Tutorials/PhantomCtf|MEG current phantom (CTF)]] * [[Tutorials/PhantomElekta|MEG current phantom (Elekta)]] <<HTML(</TD><TD>)>> * [[Tutorials/RestingOmega|MEG resting state & OMEGA database (CTF)]] * [[Tutorials/HCP-MEG|MEG Human Connectome Project (4D)]] * [[Tutorials/TutMindNeuromag|MEG median nerve (Elekta)]] * [[Tutorials/Yokogawa|MEG median nerve (Yokogawa)]] * [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] <<HTML(</TD></TR></TABLE>)>> |
| Line 98: | Line 104: |
| === Recordings === 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] 1. ICA decomposition [Under construction] 1. [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]] === Anatomy and registration === 1. [[CoordinateSystems|Brainstorm coordinate systems]] 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] [Under construction] 1. [[Tutorials/TutWarping|Warping default anatomy]] 1. [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] 1. Group analysis: Averaging [Under construction] 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] 1. [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG system]] === Source modeling === 1. [[Tutorials/TutBem|BEM with OpenMEEG]] 1. [[Tutorials/TutVolSource|Volume source estimation]] 1. [[Tutorials/TutDipScan|Computing and displaying dipoles]] 1. [[Tutorials/Beamformers|Beamforming methods]] [Under construction] 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction] === Advanced processing === 1. [[Tutorials/TutPac|Phase-amplitude coupling]] 1. [[ExportSpm8|Export volume source maps to SPM8 / SPM12]] 1. [[ExportSpm12|Export surface source maps to SPM12]] 1. [[Tutorials/TutUserProcess|How to write your own process]] === Other useful how-to's === 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] 1. [[Tutorials/KnownBugs|Known bugs]] === Tutorials from other authors === 1. This video illustrates how Brainstorm can be used for studying amygdala activity:<<BR>>[[http://www.jove.com/video/50212/how-to-detect-amygdala-activity-with-magnetoencephalography-using?status=a52218k|How to Detect Amygdala Activity with Magnetoencephalography using Source Imaging]] <<BR>>Authors: Balderston NL, Schultz DH, Baillet S, Helmstetter FJ 1. [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm") 1. [[Tutorials/WorkflowGuide|MEG analysis guidelines for McGill]] |
<<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> '''Anatomy and registration''' * [[CoordinateSystems|Brainstorm coordinate systems]] * MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], <<BR>>[[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT12]], [[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]] * [[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/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] * [[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]] * [[Tutorials/Duneuro|Realistic head model: FEM with DUNEuro]] * [[Tutorials/FemMesh|FEM mesh generation]] * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewForward|Forward models comparison]] * [[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]] '''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/Connectivity|Functional connectivity]] [TODO] * [[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]] * [[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. <<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]] <<HTML(</TD></TR></TABLE>)>> |
| Line 149: | Line 200: |
| These tutorial pages suppose you are comfortable with the basic concepts of MEG and EEG source imaging. If you're not, we engage you to read some background information, which will quickly help you getting up to speed with this field: * A non-technical overview of MEG and EEG, with an emphasis on source modeling:<<BR>> [[http://www.canada-meg-consortium.org/EN/MegIntro|Canada MEG Consortium]] * Slides from a selection of educational courses:<<BR>>[[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]] * Reference books: * [[http://www.amazon.com/MEG-Introduction-Methods-Peter-Hansen/dp/0195307232/ref=sr_1_1?ie=UTF8&qid=1324419425&sr=8-1|MEG: An Introduction to Methods]]<<BR>>Editors: P Hansen, M Kringelbach, R Salmelin, ''Oxford University Press'', 2010, 448 pages * [[http://www.amazon.com/Oxford-Handbook-Neuroscience-Library-Psychology/dp/019534216X/ref=sr_1_3?s=books&ie=UTF8&qid=1324419480&sr=1-3|The Oxford Handbook of Social Neuroscience]]<<BR>>Editors: J Decety, JT Cacioppo, ''Oxford University Press'', 2011, 1128 pages<<BR>>A draft version of the MEG chapter by Sylvain Baillet can be found [[attachment:BailletMEGDraft.pdf|here]]. '' '' * [[http://www.ncbi.nlm.nih.gov/pubmed/23046981|Good practice for conducting and reporting MEG research]], Gross et al, Neuroimage, 2013 * You can also ask us to come and organize a [[Training|training session]] at your institution, or [[http://www.bic.mni.mcgill.ca/ResearchLabsNeuroSPEED/HomePage|visit us]] to obtain training (McGill's Montreal Neurological Institute). |
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: * [[http://rdcu.be/pydB|Nature Neuroscience review paper on MEG for Human Electrophysiology and Imaging]] (Baillet S, 2017) * [[https://www.mcw.edu/Magnetoencephalography-Program-MEG/About-MEG.htm|Introduction to MEG (Medical College of Wisconsin)]] <<BR>>A non-technical overview of MEG and EEG, with an emphasis on source modeling. * [[http://www.amazon.com/MEG-Introduction-Methods-Peter-Hansen/dp/0195307232/ref=sr_1_1?ie=UTF8&qid=1324419425&sr=8-1|MEG: An Introduction to Methods]]<<BR>>Editors: P Hansen, M Kringelbach, R Salmelin, ''Oxford University Press'', 2010, 448 pages. * [[http://www.amazon.com/Oxford-Handbook-Neuroscience-Library-Psychology/dp/019534216X/ref=sr_1_3?s=books&ie=UTF8&qid=1324419480&sr=1-3|The Oxford Handbook of Social Neuroscience]]<<BR>>Editors: J Decety, JT Cacioppo, ''Oxford University Press'', 2011, 1128 pages<<BR>>A draft version of the MEG chapter by Sylvain Baillet can be found [[http://neuroimage.usc.edu/paperspdf/baillet_draft_2011.pdf|here]].'' '' * [[http://www.ncbi.nlm.nih.gov/pubmed/23046981|Good practice for conducting and reporting MEG research]], Gross et al, Neuroimage, 2013. * Slides from a selection of educational courses: [[http://megcommunity.org/education/teaching-slides|megcommunity.org]] * We can also come and organize a [[Training|training session]] at your institution, or [[http://www.bic.mni.mcgill.ca/ResearchLabsNeuroSPEED/HomePage|visit us]] at the MNI. |
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!