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| These are the most intensively used freeware software packages for EEG/MEG analysis at the CBU: | |
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| '''[http://imaging.mrc-cbu.cam.ac.uk/meg/SpmAnalysis SPM]''', developed at the [http://www.fil.ion.ucl.ac.uk/spm/ FIL] and at the [http://imaging.mrc-cbu.cam.ac.uk/meg/SpmAnalysis CBU]. | ||'''[http://imaging.mrc-cbu.cam.ac.uk/meg/SpmAnalysis SPM]''' ||'''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_overview MNE]''' ||'''[http://fieldtrip.fcdonders.nl/ Fieldtrip]''', '''[http://imaging.mrc-cbu.cam.ac.uk/imaging/FieldtripAnalysis Fieldtrip at CBU]''' || ||developed at the [http://www.fil.ion.ucl.ac.uk/spm/ FIL] and at the [http://imaging.mrc-cbu.cam.ac.uk/meg/SpmAnalysis CBU]. ||developed at [http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php MGH] ||developed at the [http://www.ru.nl/neuroimaging/ Donders centre]. || For some more details look [http://imaging.mrc-cbu.cam.ac.uk/meg/FreewarePackages here]. For an introduction and overview to different analysis approaches see our [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGday29Jan10 "MEG day" presentations]. |
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| '''[http://imaging.mrc-cbu.cam.ac.uk/meg/DansPage MNE]''', developed at [http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php MGH] | Other options are: |
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| '''[http://fieldtrip.fcdonders.nl/ Fieldtrip]''', developed at the Donders centre. | ||'''[http://sccn.ucsd.edu/eeglab EEGLAB]''' ||'''[http://nutmeg.berkeley.edu NUTMEG]''' || ||Matlab toolbox for EEG analysis (incl. ICA) || MEG/EEG analysis toolbox in conjunction with SPM8 || |
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| For some more details look [http://imaging.mrc-cbu.cam.ac.uk/meg/FreewarePackages here]. | |
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| ||[http://www.neuroscan.com/curry.cfm CURRY] || [http://www.besa.de/ BESA] || [http://www.ant-neuro.com/products/asa ASA] || [http://www.sourcesignal.com/ EMSE] || [http://www.brainproducts.com/productdetails.php?id=17 BrainVision Analyzer ] || | |
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| [http://www.neuroscan.com/curry.cfm CURRY], [http://www.besa.de/ BESA], [http://www.ant-neuro.com/products/asa ASA], [http://www.sourcesignal.com/ EMSE], [http://www.brainproducts.com/productdetails.php?id=17 BrainVision Analyzer ] | |
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The [http://imaging.mrc-cbu.cam.ac.uk/meg/NeuromagSoftware Neuromag software] is part of the [http://www.elekta.com/healthcare_international_elekta_neuromag.php Elekta Neuromag MEG system]. You can get a general idea about the analysis pathway from the [attachment:MEGAnalysisLectureJan07CBU.pdf CBU introductory lecture into MEG analysis] (the slides do not include the live software demos given at the lecture). |
The [http://imaging.mrc-cbu.cam.ac.uk/meg/NeuromagSoftware Neuromag software] is part of the [http://www.elekta.com/healthcare_international_elekta_neuromag.php Elekta Neuromag MEG system] ([http://imaging.mrc-cbu.cam.ac.uk/meg/VectorviewDescription Vectorview configuration]). You can get a general idea about the analysis pathway from the [attachment:MEGAnalysisLectureJan07CBU.pdf CBU introductory lecture into MEG analysis] (the slides do not include the live software demos given at the lecture). |
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[http://imaging.mrc-cbu.cam.ac.uk/meg/Maxfilter MaxFilter] is a pre-processing tool for MEG data, in order to remove noise sources likely to originate from outside the sensor array. |
[http://imaging.mrc-cbu.cam.ac.uk/meg/Maxfilter MaxFilter] is an essential pre-processing tool for MEG data, in order to remove noise sources likely to originate from outside the sensor array. |
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| You may want to start with a basic [http://www.mrc-cbu.cam.ac.uk/research/eeg/eeg_intro.html introduction to EEG and MEG analysis], and then look at the description of our [http://www.elekta.com/healthcare_international_elekta_neuromag.php Elekta Neuromag MEG system]. | ...you should start on our [http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners Beginners' Pages], with links to tutorials and more information on Matlab, Linux, Python etc. |
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| You should get an idea of [http://imaging.mrc-cbu.cam.ac.uk/imaging/ScientificComputing how computing is organised at the CBU]. Then you should familiarise yourself with a [http://imaging.mrc-cbu.cam.ac.uk/imaging/UsingVNC VNC viewer], or you won't be able to use our Linux cluster from your desktop PC (or from home). Your life as a neuroimager will be much easier if you have a good grasp on Linux (Unix) and Matlab. In general, I would recommend "learning by doing", but the following links will get you on your way, and may serve as useful references when you get stuck. '''Matlab: ''' You can look at [http://www.mathworks.com/academia/student_center/tutorials/launchpad.html tutorials and demos] offered by Matlab itself. This site also contains links to Matlab tutorials at some universities. You may want to start with the [http://www.mathworks.com/access/helpdesk/help/pdf_doc/matlab/getstart.pdf Getting Started] section. The short introduction to [http://imaging.mrc-cbu.cam.ac.uk/imaging/LearningMatlab Matlab for psychologists] from the University of Nottingham is also useful. You can start at the very beginning with this [http://imaging.mrc-cbu.cam.ac.uk/pdfs/matrices.pdf primer on matrices]. '''Linux (Unix): ''' This is a systematic and well-illustrated [http://www.ee.surrey.ac.uk/Teaching/Unix/ introduction to linux]. '''Python:''' Not essential for "normal" users, the scripting language [http://www.python.org/ Python] is increasingly becoming popular for its flexibility and simplicity. You could start with the [http://wiki.python.org/moin/BeginnersGuide Beginners' Guide]. '''MEG analysis software:''' Most software packages will offer tutorials and demos. They will familiarise you with basic analysis principles, visualisation options, and give you an overview of what's available to you. It makes sense to do the tutorials of software packages even if you are not planning to use them routinely. For example, MNE includes an example data set (tutorial in the [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.7.pdf manual]), and there is a [http://www.fil.ion.ucl.ac.uk/spm/data/mmfaces/ general SPM5 demo for MEG analysis], and a [http://imaging.mrc-cbu.cam.ac.uk/meg/SpmDemo tailor-made SPM5 demo for data acquired at the CBU]. And finally one last piece of advice: Talk to people! Ask questions! Try things out! And never give up... |
== Literature, Mailing Lists, Web-Sites and Events around MEG == Here you can find [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers a list of papers] and [http://imaging.mrc-cbu.cam.ac.uk/meg/MailingLists of mailing lists, web-sites and events] for various MEG-related topics. |
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Analysing data
There are several options for analysing MEG and EEG data from the Neuromag machine at the CBU:
FreewarePackages
These are the most intensively used freeware software packages for EEG/MEG analysis at the CBU:
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_overview MNE] |
[http://fieldtrip.fcdonders.nl/ Fieldtrip], [http://imaging.mrc-cbu.cam.ac.uk/imaging/FieldtripAnalysis Fieldtrip at CBU] |
|
developed at the [http://www.fil.ion.ucl.ac.uk/spm/ FIL] and at the [http://imaging.mrc-cbu.cam.ac.uk/meg/SpmAnalysis CBU]. |
developed at [http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php MGH] |
developed at the [http://www.ru.nl/neuroimaging/ Donders centre]. |
For some more details look [http://imaging.mrc-cbu.cam.ac.uk/meg/FreewarePackages here]. For an introduction and overview to different analysis approaches see our [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGday29Jan10 "MEG day" presentations].
Other options are:
[http://sccn.ucsd.edu/eeglab EEGLAB] |
[http://nutmeg.berkeley.edu NUTMEG] |
Matlab toolbox for EEG analysis (incl. ICA) |
MEG/EEG analysis toolbox in conjunction with SPM8 |
CommercialPackages
We've got one or more licenses for the following software packages:
[http://www.besa.de/ BESA] |
[http://www.sourcesignal.com/ EMSE] |
[http://www.brainproducts.com/productdetails.php?id=17 BrainVision Analyzer ] |
Neuromag Software
The [http://imaging.mrc-cbu.cam.ac.uk/meg/NeuromagSoftware Neuromag software] is part of the [http://www.elekta.com/healthcare_international_elekta_neuromag.php Elekta Neuromag MEG system] ([http://imaging.mrc-cbu.cam.ac.uk/meg/VectorviewDescription Vectorview configuration]). You can get a general idea about the analysis pathway from the [attachment:MEGAnalysisLectureJan07CBU.pdf CBU introductory lecture into MEG analysis] (the slides do not include the live software demos given at the lecture).
MaxFilter
[http://imaging.mrc-cbu.cam.ac.uk/meg/Maxfilter MaxFilter] is an essential pre-processing tool for MEG data, in order to remove noise sources likely to originate from outside the sensor array.
More info on pre-processing (e.g. trigger coding)
[http://imaging.mrc-cbu.cam.ac.uk/meg/preprocessing Pre-processing pages]
If all this is new to you...
...you should start on our [http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners Beginners' Pages], with links to tutorials and more information on Matlab, Linux, Python etc.
Literature, Mailing Lists, Web-Sites and Events around MEG
Here you can find [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers a list of papers] and [http://imaging.mrc-cbu.cam.ac.uk/meg/MailingLists of mailing lists, web-sites and events] for various MEG-related topics.