|
Size: 6367
Comment:
|
Size: 9503
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]]. | '''[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]]. |
| Line 5: | Line 7: |
| 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. 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. |
| Line 7: | Line 9: |
| '''Preparing the subject''' | <<HTML(<TABLE class="tuto-table"><TR><TD>)>> |
| Line 9: | Line 11: |
| 1. [[Tutorials/CreateProtocol|Create a new protocol]] 1. [[Tutorials/ImportAnatomy|Import the subject anatomy]] 1. [[Tutorials/ExploreAnatomy|Explore the anatomy]] |
'''Starting a new study''' |
| Line 13: | Line 13: |
| '''Reviewing and pre-processing''' | <<HTML( )>>1. [[Tutorials/CreateProtocol|Create a new protocol]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 15: | Line 15: |
| 1. [[Tutorials/ChannelFile|Coregistration MEG-MRI]] [Under construction] 1. [[Tutorials/ReviewRaw|Review continuous files]] [Under construction] 1. [[Tutorials/MontageEditor|Montage editor]] [Under construction] 1. [[Tutorials/Desktop|Desktop]] 1. [[Tutorials/EventMarkers|Edit event markers]] 1. [[Tutorials/StimDelays|Fixing stimulation delays]] 1. [[Tutorials/ArtifactsFilter|Frequency filters]] 1. Detecting artifacts 1. [[Tutorials/ArtifactsSsp|Cleaning artifacts with SSP]] 1. [[Tutorials/BadChannels|Bad channels and bad segments]] |
<<HTML( )>>2. [[Tutorials/ImportAnatomy|Import the subject anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[8] <<HTML(</FONT>)>> |
| Line 26: | Line 17: |
| '''Epoching and averaging''' [Under construction] | <<HTML( )>>3. [[Tutorials/ExploreAnatomy|Explore the anatomy]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 28: | Line 19: |
| 1. [[Tutorials/Epoching|Epoching]] 1. [[Tutorials/Averaging|Averaging trials]] 1. [[Tutorials/ExploreRecordings|Explore the average response]] 1. [[Tutorials/Colormaps|Colormaps]] |
'''Reviewing''' |
| Line 33: | Line 21: |
| '''Source modeling''' [Under construction] | <<HTML( )>>4. [[Tutorials/ChannelFile|Channel file / MRI registration]] <<HTML(<FONT color="#DDDDDD">)>>[11] <<HTML(</FONT>)>> |
| Line 35: | Line 23: |
| 1. [[Tutorials/HeadModel|Head model]] 1. [[Tutorials/NoiseCovariance|Noise covariance]] 1. [[Tutorials/SourceEstimation|Source estimation]] 1. [[Tutorials/Scouts|Scouts]] |
<<HTML( )>>5. [[Tutorials/ReviewRaw|Continuous recordings]] <<HTML(<FONT color="#DDDDDD">)>>[9] <<HTML(</FONT>)>> |
| Line 40: | Line 25: |
| '''Advanced topics''' [Under construction] | <<HTML( )>>6. [[Tutorials/MultipleWindows|Multiple windows]] <<HTML(<FONT color="#DDDDDD">)>>[5] <<HTML(</FONT>)>> |
| Line 42: | Line 27: |
| 1. [[Tutorials/TimeFrequency|Time-frequency]] 1. [[Tutorials/Statistics|Statistics]] 1. [[Tutorials/Connectivity|Connectivity]] 1. [[Tutorials/Scripting|Advanced scripting]] |
<<HTML( )>>7. [[Tutorials/EventMarkers|Event markers]] <<HTML(<FONT color="#DDDDDD">)>>[10] <<HTML(</FONT>)>> |
| Line 47: | Line 29: |
| == Complete analysis of other datasets == | '''Pre-processing''' <<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( )>>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>)>> '''Epoching and averaging''' <<HTML( )>>15. [[Tutorials/Epoching|Import epochs]] <<HTML(<FONT color="#DDDDDD">)>>[7] <<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">)>>[6] <<HTML(</FONT>)>> <<HTML( )>>19. [[Tutorials/ChannelClusters|Clusters of sensors]] <<HTML(<FONT color="#DDDDDD">)>>[4] <<HTML(</FONT>)>> <<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></TR></TABLE>)>> == Other analysis scenarios == |
| Line 50: | Line 90: |
| 1. [[Tutorials/MedianNerveCtf|MEG median nerve (CTF)]] [Under construction] | |
| Line 51: | Line 92: |
| 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag|MEG median nerve (Elekta-Neuromag)]] | 1. [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag|MEG median nerve (Elekta-Neuromag)]] [Under construction] |
| Line 55: | Line 96: |
| === 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]] |
|
| Line 57: | Line 106: |
| 1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegCIVET|CIVET]] 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] |
1. MRI segmentation: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainSuite|BrainSuite]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegCIVET|CIVET]] 1. [[Tutorials/DefaultAnatomy|Using the anatomy templates]] [Under construction] |
| Line 62: | Line 111: |
| 1. [[Tutorials/CoregisterSubjects|Group studies: Subjects coregistration]] | 1. [[Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]] |
| Line 64: | Line 113: |
| 1. [[Tutorials/MegCoreg|Co-registration of MEG runs]] [Under construction] | 1. Group analysis: Averaging [Under construction] |
| Line 68: | Line 117: |
=== Graphical 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 85: | Line 129: |
| === Functional connectivity === | === Advanced processing === |
| Line 88: | Line 132: |
| === Statistics === | |
| Line 91: | Line 134: |
| 1. [[Tutorials/TutUserProcess|How to write your own process]] | |
| Line 97: | Line 141: |
| === 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 98: | Line 145: |
=== 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
[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 background literature.
To get a quick overview of the software interface, you can watch this introduction video.
Get started
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.
| 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 21. Noise covariance 23. Scouts Advanced signal processing 24. Time-frequency 25. Statistics 26. Connectivity 27. Phase-amplitude coupling Scripting |
Other analysis scenarios
MEG median nerve (CTF) [Under construction]
MEG median nerve (Elekta-Neuromag) [Under construction]
Advanced tutorials
Recordings
Montage editor [Under construction]
- ICA decomposition [Under construction]
Anatomy and registration
MRI segmentation: FreeSurfer, BrainSuite, BrainVISA, CIVET
Using the anatomy templates [Under construction]
- Group analysis: Averaging [Under construction]
Source modeling
Beamforming methods [Under construction]
Maximum Entropy on the Mean (MEM) [Under construction]
Advanced processing
Other useful how-to's
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!