|
Size: 9559
Comment:
|
Size: 10164
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/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 5: | 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. | 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]]. |
| Line 15: | 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 29: | Line 29: |
| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> | <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 31: | Line 31: |
| <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> | <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
| Line 33: | Line 33: |
| <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> | <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[15] <<HTML(</FONT>)>> |
| Line 37: | 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 43: | Line 43: |
| <<HTML(</TD><TD>)>> |
|
| Line 45: | Line 47: |
| <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> | <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 51: | Line 53: |
| <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> | <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
| Line 54: | Line 56: |
'''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>)>> <<HTML(</TD></TR></TABLE>)>> == Other analysis scenarios == <<HTML(<TABLE class="tuto-table"><TR><TD>)>> * [[Tutorials/Epilepsy|EEG and epilepsy]] [TODO] * [[Tutorials/VisualSingle|MEG visual: single subject (Elekta)]] * [[Tutorials/VisualGroup|MEG visual: group study (Elekta)]] * [[Tutorials/PhantomCtf|MEG current phantom (CTF)]] * [[Tutorials/PhantomElekta|MEG current phantom (Elekta)]] * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] <<HTML(</TD><TD>)>> * [[Tutorials/TutMindNeuromag|MEG median nerve (Elekta)]] [TODO] * [[Tutorials/Yokogawa|MEG median nerve (Yokogawa)]] [TODO] * [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] [TODO] * [[Tutorials/Auditory|MEG auditory (CTF)]] [TODO] * [[Tutorials/Resting|MEG resting state / PAC (CTF)]] [TODO] <<HTML(</TD></TR></TABLE>)>> == Advanced tutorials == <<HTML(<TABLE class="tuto-table"><TR><TD>)>> '''Recordings''' * [[Tutorials/MontageEditor|Montage editor]] [TODO] * [[Tutorials/SSPCookbook|Cleaning artifacts using SSP: examples]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime|Real-time head-tracking]] * [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] <<HTML(</TD><TD>)>> '''Advanced processing''' * [[Tutorials/Connectivity|Functional connectivity]] [TODO] * [[Tutorials/TutPac|Phase-amplitude coupling]] * [[ExportSpm8|Export volume sources to SPM8/SPM12]] * [[ExportSpm12|Export surface sources to SPM12]] * [[Tutorials/Decoding|Decoding conditions (MVPA)]] * [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] * [[Tutorials/TutUserProcess|How to write your own process]] <<HTML(</TD></TR><TR><TD>)>> '''Anatomy and registration''' * [[CoordinateSystems|Brainstorm coordinate systems]] * [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] * [[Tutorials/DefaultAnatomy|Using the anatomy templates]] * [[Tutorials/TutWarping|Warping default anatomy]] * [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] * [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] * [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG]] |
|
| Line 59: | Line 140: |
| <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] [Under construction] <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise covariance]] [Under construction] <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] [Under construction] <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] [Under construction] '''Advanced signal processing''' <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] [Under construction] <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] [Under construction] <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] [Under construction] <<HTML( )>>27. Phase-amplitude coupling [Under construction] '''Scripting''' <<HTML( )>>28. [[Tutorials/Scripting|Complete tutorial script]] [Under construction] <<HTML( )>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]] |
* [[Tutorials/TutBem|BEM with OpenMEEG]] * [[Tutorials/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] [TODO] * [[Tutorials/TutDipScan|Dipoles: Scanning and importing]] [TODO] * [[Tutorials/DipoleFitting|Dipoles: FieldTrip dipole fitting]] * [[Tutorials/Beamformers|Beamforming methods]] [TODO] * [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] * [[Tutorials/EpilepsyBest|MEM Epilepsy]] [TODO] |
| Line 85: | Line 151: |
| == Other analysis scenarios == 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)]] |
'''Other useful how-to's''' |
| Line 93: | Line 153: |
| == Advanced tutorials == === 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]] |
* [[CiteBrainstorm|How to cite Brainstorm]] * [[Tutorials/KnownBugs|Known bugs]] |
| Line 100: | Line 156: |
| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime|Real-time head-tracking for adjusting head position]] | '''Tutorials from other authors''' |
| Line 102: | Line 158: |
| === 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] |
* Video tutorial: [[http://www.jove.com/video/50212/how-to-detect-amygdala-activity-with-magnetoencephalography-using?status=a52218k|How to detect amygdala activity with MEG using source imaging]] |
| Line 107: | Line 160: |
| 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]] |
* [[http://meg.aalip.jp/matlab/index.html|A tutorial in Japanese]] (click on the menu "Brainstorm") |
| Line 147: | Line 165: |
| * 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]] | * [[http://www.canada-meg-consortium.org/EN/MegIntro|Canada MEG consortium: Basics of MEG]]<<BR>>A non-technical overview of MEG and EEG, with an emphasis on source modeling. |
| Line 149: | Line 167: |
| * Slides from a selection of educational courses:<<BR>>[[http://megcommunity.org/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]] | * [[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. |
| Line 151: | Line 169: |
| * 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]]. '' '' |
| Line 154: | Line 171: |
| * [[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. |
| Line 156: | Line 173: |
| * [[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/index.php?option=com_content&view=article&id=27&Itemid=13|megcommunity.org]] |
| Line 158: | Line 175: |
| * 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). | * 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.
Some sections are still being edited or under review: Editing process.
| 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
| Recordings | Advanced processing |
| Anatomy and registration | Source modeling
|
Other useful how-to's
Tutorials from other authors
Video tutorial: How to detect amygdala activity with MEG using source imaging
A tutorial in Japanese (click on the menu "Brainstorm")
Background readings
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:
Canada MEG consortium: Basics of MEG
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!