|
Size: 7862
Comment:
|
Size: 10221
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. |
| Line 9: | Line 9: |
| ==== Starting a new study ==== <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] |
'''Starting a new study''' |
| Line 12: | Line 11: |
| <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] | <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 14: | Line 13: |
| <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] | <<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
| Line 16: | Line 15: |
| ==== Reviewing ==== <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file & MRI coregistration]] |
<<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 19: | Line 17: |
| <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] | '''Reviewing''' |
| Line 21: | Line 19: |
| <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] | <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
| Line 23: | Line 21: |
| <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] | <<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 25: | Line 23: |
| ==== Pre-processing ==== <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] [Under construction] |
<<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
| Line 28: | Line 25: |
| <<HTML( )>>9. [[Tutorials/ArtifactsFilter|Frequency filters]] [Under construction] | <<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 30: | Line 27: |
| <<HTML( )>>10. [[Tutorials/BadChannels|Bad channels]] [Under construction] | '''Pre-processing''' |
| Line 32: | Line 29: |
| <<HTML( )>>11. [[Tutorials/ArtifactsDetect|Artifact detection]] [Under construction] | <<HTML( )>>8. [[Tutorials/StimDelays|Stimulation delays]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 34: | Line 31: |
| <<HTML( )>>12. [[Tutorials/ArtifactsSsp|Artifact cleaning with SSP]] [Under construction] | <<HTML( )>>9. [[Tutorials/PipelineEditor|Select files / Run processes]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 36: | Line 33: |
| <<HTML( )>>13. [[Tutorials/BadSegments|Additional bad segments]] [Under construction] | <<HTML( )>>10. [[Tutorials/ArtifactsFilter|Power spectrum / Frequency filters]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> <<HTML( )>>11. [[Tutorials/BadChannels|Bad channels]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> <<HTML( )>>12. [[Tutorials/ArtifactsDetect|Artifact detection]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> <<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 40: | Line 45: |
| ==== Epoching and averaging [Under construction] ==== <<HTML( )>>14. [[Tutorials/Epoching|Import epochs]] |
'''Epoching and averaging''' |
| Line 43: | Line 47: |
| <<HTML( )>>15. [[Tutorials/Averaging|Average response]] | <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
| Line 45: | Line 49: |
| <<HTML( )>>16. [[Tutorials/ExploreRecordings|Exploring the average response]] | <<HTML( )>>16. [[Tutorials/Averaging|Average response]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<HTML(</FONT>)>> |
| Line 47: | Line 51: |
| <<HTML( )>>17. 2D/3D topography | <<HTML( )>>17. [[Tutorials/ExploreRecordings|Visual exploration]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 49: | Line 53: |
| <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] | <<HTML( )>>18. [[Tutorials/Colormaps|Colormaps]] <<HTML(<FONT color="#DDDDDD">)>>[6] <<HTML(</FONT>)>> |
| Line 51: | Line 55: |
| ==== Source modeling [Under construction] ==== <<HTML( )>>19. [[Tutorials/HeadModel|Head model]] |
<<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> |
| Line 54: | Line 57: |
| <<HTML( )>>20. [[Tutorials/NoiseCovariance|Noise covariance]] | '''Source modeling''' |
| Line 56: | Line 59: |
| <<HTML( )>>21. [[Tutorials/SourceEstimation|Source estimation]] | <<HTML( )>>20. [[Tutorials/HeadModel|Head model]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
| Line 58: | Line 61: |
| <<HTML( )>>22. [[Tutorials/Scouts|Scouts]] | <<HTML( )>>21. [[Tutorials/NoiseCovariance|Noise/data covariance]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
| Line 60: | Line 63: |
| ==== Advanced topics [Under construction] ==== <<HTML( )>>23. [[Tutorials/TimeFrequency|Time-frequency]] |
<<HTML( )>>22. [[Tutorials/SourceEstimation|Source estimation]] [Under construction] |
| Line 63: | Line 65: |
| <<HTML( )>>24. [[Tutorials/Statistics|Statistics]] | <<HTML( )>>23. [[Tutorials/Scouts|Scouts]] <<HTML(<FONT color="#DDDDDD">)>>[17] <<HTML(</FONT>)>> |
| Line 65: | Line 67: |
| <<HTML( )>>25. [[Tutorials/Connectivity|Connectivity]] | '''Advanced processing''' |
| Line 67: | Line 69: |
| <<HTML( )>>26. Phase-amplitude coupling | <<HTML( )>>24. [[Tutorials/TimeFrequency|Time-frequency]] <<HTML(<FONT color="#DDDDDD">)>>[22] <<HTML(</FONT>)>> |
| Line 69: | Line 71: |
| <<HTML( )>>27. [[Tutorials/Scripting|Advanced scripting]] | <<HTML( )>>25. [[Tutorials/Difference|Difference]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 71: | Line 73: |
| <<HTML( )>>28. Complete tutorial script | <<HTML( )>>26. [[Tutorials/Statistics|Statistics]] <<HTML(<FONT color="#DDDDDD">)>>[27] <<HTML(</FONT>)>> [Under construction] |
| Line 73: | Line 75: |
| <<HTML( )>>29. Summary | <<HTML( )>>27. [[Tutorials/Connectivity|Connectivity]] [Under construction] <<HTML( )>>28. [[Tutorials/Scripting|Scripting]] [Under construction] |
| Line 77: | 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 81: | 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/KIT)]] 1. [[Tutorials/TutMindNeuromag|MEG median nerve (Elekta-Neuromag)]] [Under construction] 1. [[Tutorials/Resting|MEG resting state (CTF)]] 1. [[Tutorials/VisualSingle|MEG visual single subject (Elekta-Neuromag)]] [Under construction] 1. [[Tutorials/VisualGroup|MEG visual group study (Elekta-Neuromag)]] [Under construction] 1. MEG steady-state visual (CTF) |
| Line 86: | Line 93: |
| === Interface === | === Recordings === |
| Line 88: | Line 95: |
| 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]] |
|
| Line 91: | Line 103: |
| 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegCIVET|CIVET]] 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] [Under construction] |
1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] |
| Line 96: | Line 108: |
| 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] 1. Group studies: Averaging |
1. [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] |
| Line 102: | Line 112: |
=== 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]] |
|
| Line 113: | Line 118: |
| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|Deep cerebral structures]] [Under construction] |
|
| Line 114: | Line 121: |
1. [[Tutorials/DipoleFitting|Dipole fitting with FieldTrip]] |
|
| Line 117: | Line 126: |
| 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] [Under construction] | 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM)]] |
| Line 119: | Line 128: |
| === Functional connectivity === | 1. [[Tutorials/TutBEst|Maximum Entropy on the Mean (MEM) - Epilepsy]] === Advanced processing === |
| Line 122: | Line 133: |
| === Statistics === | |
| Line 125: | Line 135: |
| 1. [[Tutorials/Decoding|Decoding conditions (MVPA)]] 1. [[Tutorials/MicrostatesCena|Microstate segmentation with CENA]] 1. [[Tutorials/TutUserProcess|How to write your own process]] |
|
| Line 127: | Line 140: |
| 1. [[Tutorials/IPythonNotebook|Brainstorm on IPython Notebook]] [Under construction] | |
| Line 131: | Line 145: |
| 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 132: | Line 151: |
=== 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.
| Starting a new study 1. Create a new protocol [9] 2. Import the subject anatomy [8] 3. Explore the anatomy [10] Reviewing 4. Channel file / MRI registration [11] 5. Continuous recordings [9] 6. Multiple windows [5] 7. Event markers [10] Pre-processing 8. Stimulation delays [10] 9. Select files / Run processes [10] 10. Power spectrum / Frequency filters [11] 11. Bad channels [6] 12. Artifact detection [7] 13. Artifact cleaning with SSP [16] 14. Additional bad segments [7] | Epoching and averaging 15. Import epochs [7] 16. Average response [7] 17. Visual exploration [10] 18. Colormaps [6] 19. Clusters of sensors [4] Source modeling 20. Head model [8] 21. Noise/data covariance [8] 22. Source estimation [Under construction] 23. Scouts [17] Advanced processing 24. Time-frequency [22] 25. Difference [9] 26. Statistics [27] [Under construction] 27. Connectivity [Under construction] 28. Scripting [Under construction] |
Other analysis scenarios
MEG median nerve (CTF) [Under construction]
MEG median nerve (Elekta-Neuromag) [Under construction]
MEG visual single subject (Elekta-Neuromag) [Under construction]
MEG visual group study (Elekta-Neuromag) [Under construction]
- MEG steady-state visual (CTF)
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
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!