|
Size: 7756
Comment:
|
Size: 10601
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.<<BR>>Some sections are still being edited or under review: [[Tutorials/Review|Editing process]]. |
| 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]] | <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 31: | Line 31: |
| <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files and run processes]] | <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
| Line 33: | Line 33: |
| <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Frequency filters]] | <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[15] <<HTML(</FONT>)>> |
| Line 35: | Line 35: |
| <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] [Under construction] | <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> |
| Line 37: | Line 37: |
| <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] [Under construction] | <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
| Line 39: | Line 39: |
| <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] [Under construction] | <<HTML( )>>13. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] <<HTML(<FONT color="#DDDDDD">)>>[16] <<HTML(</FONT>)>> |
| Line 41: | Line 41: |
| <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] [Under construction] | <<HTML( )>>14. [[Tutorials/BadSegments|Additional bad segments]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<HTML(</TD><TD>)>> |
| Line 45: | Line 47: |
| <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] | <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 47: | Line 49: |
| <<HTML( )>>16. [[Tutorials/Averaging|Average response]] | <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
| Line 49: | Line 51: |
| <<HTML( )>>17. [[Tutorials/ExploreRecordings|Exploring the average response]] | <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 51: | Line 53: |
| <<HTML( )>>18. 2D/3D topography | <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
| Line 53: | Line 55: |
| <<HTML( )>>19. [[Tutorials/Colormaps|Colormaps]] <<HTML(</TD><TD>)>> |
<<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> |
| Line 59: | Line 59: |
| <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] | <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 61: | Line 61: |
| <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise covariance]] | <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
| Line 63: | Line 63: |
| <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] | <<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] <<HTML(<FONT color="#DDDDDD">)>>[28] <<HTML(</FONT>)>> |
| Line 65: | Line 65: |
| <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] | <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>>[17] <<HTML(</FONT>)>> |
| Line 67: | Line 67: |
| '''Advanced signal processing''' | '''Advanced processing''' |
| Line 69: | Line 69: |
| <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] | <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[22] <<HTML(</FONT>)>> |
| Line 71: | Line 71: |
| <<HTML( )>>25. [[Tutorials/Statistics|Statistics]] | <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 73: | Line 73: |
| <<HTML( )>>26. [[Tutorials/Connectivity|Connectivity]] | <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>>[25] <<HTML(</FONT>)>> [Under construction] |
| Line 75: | Line 75: |
| <<HTML( )>>27. Phase-amplitude coupling | <<HTML( )>>27. [[Tutorials/Workflows|Workflows]] [Under construction] |
| Line 77: | Line 77: |
| '''Scripting''' <<HTML( )>>28. [[Tutorials/Scripting|Complete tutorial script]] <<HTML( )>>29. [[Tutorials/AllIntroduction|All the tutorials on the same page]] |
<<HTML( )>>28. [[Tutorials/Scripting|Scripting]] [Under construction] |
| Line 85: | 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]] |
== Other analysis scenarios == 1. [[Tutorials/Epilepsy|EEG and epilepsy]] 1. [[Tutorials/Auditory|MEG auditory tutorial (CTF)]] |
| Line 89: | Line 85: |
| 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]] |
1. [[Tutorials/Yokogawa|MEG median nerve (Yokogawa)]] 1. [[Tutorials/TutMindNeuromag|MEG median nerve (Elekta)]] [Under construction] 1. [[Tutorials/Resting|MEG resting state (CTF)]] 1. [[Tutorials/VisualSingle|MEG visual single subject (Elekta)]] [Under construction] 1. [[Tutorials/VisualGroup|MEG visual group study (Elekta)]] [Under construction] 1. [[Tutorials/PhantomCtf|MEG current phantom (CTF)]] 1. [[Tutorials/PhantomElekta|MEG current phantom (Elekta)]] 1. [[Tutorials/NIRSFingerTapping|NIRS finger tapping]] |
| Line 94: | Line 95: |
| === Interface === | === Recordings === |
| Line 96: | Line 97: |
| 1. [[Tutorials/ICA|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]] 1. [[Tutorials/EyetrackSynchro|Synchronization with eye tracker]] |
|
| Line 100: | Line 108: |
| 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] [Under construction] | 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] |
| Line 104: | Line 112: |
| 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] 1. Group studies: Averaging |
1. [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] |
| Line 110: | Line 116: |
=== Scripting === 1. [[Tutorials/TutUserProcess|How to write your own process]] |
|
| Line 119: | Line 122: |
| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] [Under construction] |
|
| Line 120: | Line 125: |
1. [[Tutorials/DipoleFitting|Dipole fitting with FieldTrip]] |
|
| Line 123: | Line 130: |
| 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction] | 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] |
| Line 125: | Line 132: |
| === Functional connectivity === | 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM) - Epilepsy]] === Advanced processing === 1. [[Tutorials/Connectivity|Functional connectivity]] [Under construction] |
| Line 128: | Line 138: |
| === Statistics === | |
| Line 131: | Line 140: |
| 1. [[Tutorials/Decoding|Decoding conditions (MVPA)]] 1. [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] 1. [[Tutorials/TutUserProcess|How to write your own process]] |
|
| Line 133: | Line 145: |
| 1. [[Tutorials/IPythonNotebook|Brainstorm on IPython Notebook]] [Under construction] | |
| Line 137: | Line 150: |
| 1. [[Tutorials/AllIntroduction|All the introduction tutorials on the same page]] === 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") |
|
| Line 138: | Line 156: |
=== 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 |
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.
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 [22] 25. Difference [9] 26. Statistics [25] [Under construction] 27. Workflows [Under construction] 28. Scripting [Under construction] |
Other analysis scenarios
MEG median nerve (CTF) [Under construction]
MEG median nerve (Elekta) [Under construction]
MEG visual single subject (Elekta) [Under construction]
MEG visual group study (Elekta) [Under construction]
Advanced tutorials
Recordings
Montage editor [Under construction]
?ICA decomposition [Under construction]
Anatomy and registration
MRI segmentation: FreeSurfer, BrainSuite, BrainVISA, CIVET
Source modeling
Deep cerebral structures [Under construction]
Beamforming methods [Under construction]
Advanced processing
Functional connectivity [Under construction]
Other useful how-to's
?Brainstorm on IPython Notebook [Under construction]
Tutorials from other authors
This video illustrates how Brainstorm can be used for studying amygdala activity:
How to Detect Amygdala Activity with Magnetoencephalography using Source Imaging
Authors: Balderston NL, Schultz DH, Baillet S, Helmstetter FJA tutorial in Japanese (click on the menu "Brainstorm")
?MEG analysis guidelines for McGill
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:
A non-technical overview of MEG and EEG, with an emphasis on source modeling:
Canada MEG ConsortiumSlides from a selection of educational courses:
megcommunity.org- Reference books:
MEG: An Introduction to Methods
Editors: P Hansen, M Kringelbach, R Salmelin, Oxford University Press, 2010, 448 pagesThe 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
You can also ask us to come and organize a training session at your institution, or visit us to obtain training (McGill's Montreal Neurological Institute).
Now you are well equipped to go through the software tutorial, Enjoy!