|
Size: 7787
Comment:
|
Size: 9790
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]]. | 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 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 7: | Line 7: |
| <<HTML(<TABLE class="tuto-table"><TR><TD>)>> | <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> |
| Line 11: | Line 11: |
| <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] | <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 13: | Line 13: |
| <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] | <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
| Line 15: | Line 15: |
| <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] | <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> |
| Line 19: | Line 19: |
| <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file & MRI coregistration]] | <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
| Line 21: | Line 21: |
| <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] | <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 23: | Line 23: |
| <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] | <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
| Line 25: | Line 25: |
| <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] | <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 29: | Line 29: |
| <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] [Under construction] | <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 31: | Line 31: |
| <<HTML( )>>9. [[Tutorials/ArtifactsFilter|Frequency filters]] [Under construction] | <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
| Line 33: | Line 33: |
| <<HTML( )>>10. [[Tutorials/BadChannels|Bad channels]] [Under construction] | <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[15] <<HTML(</FONT>)>> |
| Line 35: | Line 35: |
| <<HTML( )>>11. [[Tutorials/ArtifactsDetect|Artifact detection]] [Under construction] | <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> |
| Line 37: | Line 37: |
| <<HTML( )>>12. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] [Under construction] | <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
| Line 39: | Line 39: |
| <<HTML( )>>13. [[Tutorials/BadSegments|Additional bad segments]] [Under construction] | <<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>)>> |
| Line 45: | Line 47: |
| <<HTML( )>>14. [[Tutorials/Epoching|Import epochs]] | <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 47: | Line 49: |
| <<HTML( )>>15. [[Tutorials/Averaging|Average response]] | <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
| Line 49: | Line 51: |
| <<HTML( )>>16. [[Tutorials/ExploreRecordings|Exploring the average response]] | <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 51: | Line 53: |
| <<HTML( )>>17. 2D/3D topography | <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
| Line 53: | Line 55: |
| <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] | <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> |
| Line 57: | Line 59: |
| <<HTML( )>>19. [[Tutorials/HeadModel|Head model]] | <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 59: | Line 61: |
| <<HTML( )>>20. [[Tutorials/NoiseCovariance|Noise covariance]] | <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
| Line 61: | Line 63: |
| <<HTML( )>>21. [[Tutorials/SourceEstimation|Source estimation]] | <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> '''[TODO]''' |
| Line 63: | Line 65: |
| <<HTML( )>>22. [[Tutorials/Scouts|Scouts]] | <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>>[17] <<HTML(</FONT>)>> |
| Line 65: | Line 67: |
| '''Advanced topics''' | '''Advanced processing''' |
| Line 67: | Line 69: |
| <<HTML( )>>23. [[Tutorials/TimeFrequency|Time-frequency]] | <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[33] <<HTML(</FONT>)>> |
| Line 69: | Line 71: |
| <<HTML( )>>24. [[Tutorials/Statistics|Statistics]] | <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>>[13] <<HTML(</FONT>)>> |
| Line 71: | Line 73: |
| <<HTML( )>>25. [[Tutorials/Connectivity|Connectivity]] | <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>>[30] <<HTML(</FONT>)>> |
| Line 73: | Line 75: |
| <<HTML( )>>26. Phase-amplitude coupling | <<HTML( )>>27. [[Tutorials/Workflows|Workflows]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 75: | Line 77: |
| <<HTML( )>>27. [[Tutorials/Scripting|Advanced scripting]] <<HTML( )>>28. Complete tutorial script <<HTML( )>>29. Summary |
<<HTML( )>>28. [[Tutorials/Scripting|Scripting]] <<HTML(<FONT color="#DDDDDD">)>>[31] <<HTML(</FONT>)>> |
| Line 83: | Line 81: |
| == Complete analysis of other datasets == 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG and epilepsy]] 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory|MEG auditory tutorial]] 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]] |
== Other analysis scenarios == <<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> * [[Tutorials/Epilepsy|EEG and epilepsy]] * [[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)]] <<HTML(</TD><TD>)>> * [[Tutorials/RestingOmega|MEG resting state & OMEGA database (CTF)]] '''[T] ''' * [[Tutorials/TutMindNeuromag|MEG median nerve (Elekta)]] * [[Tutorials/Yokogawa|MEG median nerve (Yokogawa)]] * [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] * [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] [TODO] * [[Tutorials/HCP-MEG|MEG Human Connectome Project (4D)]] '''[TODO]''' <<HTML(</TD></TR></TABLE>)>> |
| Line 92: | Line 102: |
| === Interface === 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] |
<<HTML(<TABLE class="tuto-table"><TR><TD width=350>)>> |
| Line 95: | Line 104: |
| === Anatomy and registration === 1. [[CoordinateSystems|Brainstorm coordinate systems]] 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegCIVET|CIVET]] 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] [Under construction] |
'''Anatomy and registration''' |
| Line 100: | Line 106: |
| 1. [[Tutorials/TutWarping|Warping default anatomy]] | * [[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 the anatomy templates]] * [[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 102: | Line 114: |
| 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] | '''Recordings''' |
| Line 104: | Line 116: |
| 1. Group studies: Averaging | * [[Tutorials/MontageEditor|Montage editor]] * [[Tutorials/SSPCookbook|SSP cookbook]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/MovementDetect|Detect subject movements]] * [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] |
| Line 106: | Line 121: |
| 1. [[Tutorials/TutDigitize|Digitize EEG electrodes and head shape]] 1. [[Tutorials/TutRealtime|Real-time head positioning in the CTF MEG system]] |
'''Software''' |
| Line 109: | Line 123: |
| === Scripting === 1. [[SelectFiles|Selecting files in the database]] 1. [[Tutorials/TutRawScript|Full analysis with one script]] 1. [[Tutorials/TutUserProcess|How to write your own process]] |
* [[CiteBrainstorm|How to cite Brainstorm]] [TODO] * [[Tutorials/KnownBugs|Known bugs]] |
| Line 114: | Line 126: |
| === Source modeling === 1. [[Tutorials/TutBem|BEM with OpenMEEG]] |
<<HTML(</TD><TD>)>> |
| Line 117: | Line 128: |
| 1. [[Tutorials/TutVolSource|Volume source estimation]] | '''Source modeling''' |
| Line 119: | Line 130: |
| 1. [[Tutorials/TutDipScan|Computing and displaying dipoles]] | * [[Tutorials/TutBem|Realistic head model: BEM with OpenMEEG]] * [[Tutorials/TutVolSource|Volume source estimation]] * [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] * [[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]] |
| Line 121: | Line 138: |
| 1. [[Tutorials/Beamformers|Beamforming methods]] [Under construction] | '''Advanced processing''' |
| Line 123: | Line 140: |
| 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction] | * [[Tutorials/TutUserProcess|How to write your own process]] * [[Tutorials/Decoding|Decoding conditions (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/MicrostatesCena|Microstate segmentation with CENA]] * [[ExportSpm8|Export volume sources to SPM8/SPM12]] * [[ExportSpm12|Export surface sources to SPM12]] |
| Line 125: | Line 150: |
| === Functional connectivity === 1. [[Tutorials/TutPac|Phase-amplitude coupling]] === Statistics === 1. [[ExportSpm8|Export volume source maps to SPM8 / SPM12]] 1. [[ExportSpm12|Export surface source maps to SPM12]] === Other useful how-to's === 1. [[CiteBrainstorm|How to cite Brainstorm in your publications]] 1. [[Tutorials/KnownBugs|Known bugs]] 1. [[Tutorials/WorkflowGuide|MEG analysis guidelines for McGill]] === Examples === 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 |
<<HTML(</TD></TR></TABLE>)>> |
| Line 145: | Line 155: |
| * 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 147: | Line 157: |
| * 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 149: | Line 159: |
| * 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 [[http://neuroimage.usc.edu/paperspdf/baillet_draft_2011.pdf|here]].'' '' |
| Line 152: | Line 161: |
| * [[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 154: | Line 163: |
| * [[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 156: | Line 165: |
| * 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] [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
| Source modeling Advanced processing |
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!