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MEG/EEG data analysis in [http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php MNE software] uses information from structural [http://imaging.mrc-cbu.cam.ac.uk/imaging/ImagingSequences MRI] images, which have to be pre-processed using [http://surfer.nmr.mgh.harvard.edu/ Freesurfer]. You may want to start with the tutorial based on an example data set, as described in the MNE manual ([http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf Version 2.6] or [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.7.pdf Version 2.7]; chapter 12), or look at [http://www.martinos.org/mne/ some example scripts]. Freesurfer is accompanied by extensive [http://surfer.nmr.mgh.harvard.edu/fswiki Freesurfer Wiki pages], containing a [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide Getting Started] and [http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ FAQ] section. You will need some experience with Linux commands and scripting, which you may find on our [http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners beginners' pages]. | MEG/EEG data analysis in [http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php MNE software] uses information from structural [wiki:CbuImaging:ImagingSequences MRI] images, which have to be pre-processed using [http://surfer.nmr.mgh.harvard.edu/ Freesurfer]. You may want to start with the tutorial based on an example data set, as described in the MNE manual ([http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf Version 2.6] or [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.7.pdf Version 2.7]; chapter 12), or look at [http://www.martinos.org/mne/ some example scripts]. Freesurfer is accompanied by extensive [http://surfer.nmr.mgh.harvard.edu/fswiki Freesurfer Wiki pages], containing a [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide Getting Started] and [http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ FAQ] section. You will need some experience with Linux commands and scripting, which you may find on our [wiki:meg:Beginners beginners' pages]. |
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If you've never used shell scripts before, this [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/Primer_ShellScripting primer on shell scripting] will get you on the way. | If you've never used shell scripts before, this [wiki:CbuMeg:AnalyzingData/Primer_ShellScripting primer on shell scripting] will get you on the way. |
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There is also a short description on how to [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_prepare prepare for MNE analysis and access the Matlab toolbox]. | There is also a short description on how to [wiki:CbuMeg:AnalyzingData/MNE_prepare prepare for MNE analysis and access the Matlab toolbox]. |
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The parameters in the following examples are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the MNE manual ([http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf V2.6], [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.7.pdf V 2.7]), [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers reading papers], and [http://imaging.mrc-cbu.cam.ac.uk/imaging/ImagersInterestGroup discussions] with more experienced researchers. You may also want to subscribe to the [http://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis MNE mailing list]. | The parameters in the following examples are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the MNE manual ([http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf V2.6], [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.7.pdf V 2.7]), [wiki:CbuMeg:MEGpapers reading papers], and [wiki:CbuImaging:ImagersInterestGroup discussions] with more experienced researchers. You may also want to subscribe to the [http://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis MNE mailing list]. |
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1) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_preprocessing Pre-process your MRI Data Using Freesurfer] | 1) [wiki:CbuMeg:AnalyzingData/MNE_MRI_preprocessing Pre-process your MRI Data Using Freesurfer] |
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2) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Create Source Space and Head Surfaces] (incl. aligning coordinate systems) | 2) [wiki:CbuMeg:AnalyzingData/MNE_MRI_processing Create Source Space and Head Surfaces] (incl. aligning coordinate systems) |
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3) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution Compute the Forward Solution and BEM] | 3) [wiki:CbuMeg:AnalyzingData/MNE_ForwardSolution Compute the Forward Solution and BEM] |
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4) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_CovarianceMatrix Compute the Noise Covariance Matrix] | 4) [wiki:CbuMeg:AnalyzingData/MNE_CovarianceMatrix Compute the Noise Covariance Matrix] |
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5) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_InverseOperator Compute the Inverse Operator] | 5) [wiki:CbuMeg:AnalyzingData/MNE_InverseOperator Compute the Inverse Operator] |
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6) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Averaging Averaging MEG data] (incl. correcting EEG location information, Marking bad channels) | 6) [wiki:CbuMeg:AnalyzingData/MNE_Averaging Averaging MEG data] (incl. correcting EEG location information, Marking bad channels) |
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7) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Compute the Source Estimates] (incl. average cortical surface, grand-averaging) | 7) [wiki:CbuMeg:AnalyzingData/MNE_ComputeEstimates Compute the Source Estimates] (incl. average cortical surface, grand-averaging) |
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8) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Labels ROI/Label analysis] (incl. pre-defined labels, make-your-own) | 8) [wiki:CbuMeg:AnalyzingData/MNE_Labels ROI/Label analysis] (incl. pre-defined labels, make-your-own) |
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[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_AllInOne List of Most Relevant MNE Commands] | [wiki:CbuMeg:AnalyzingData/MNE_AllInOne List of Most Relevant MNE Commands] |
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1) You may want to [http://imaging.mrc-cbu.cam.ac.uk/meg/PreProcessing filter] or [http://imaging.mrc-cbu.cam.ac.uk/meg/Maxfilter maxfilter] ([http://imaging.mrc-cbu.cam.ac.uk/meg/MaxfilterMatlabScript Matlab script]) your data before averaging | 1) You may want to [wiki:CbuMeg:PreProcessing filter] or [wiki:CbuMeg:Maxfilter maxfilter] ([wiki:CbuMeg:MaxfilterMatlabScript Matlab script]) your data before averaging |
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2) At the moment, MNE does not provide any statistics tools (but see MNE-Python tools, point 11). You can use [http://imaging.mrc-cbu.cam.ac.uk/meg/SensorStats sensor stats] implemented in SPM ([http://imaging.mrc-cbu.cam.ac.uk/meg/SensorSpm SensorSPM]) for statistics in sensor space. | 2) At the moment, MNE does not provide any statistics tools (but see MNE-Python tools, point 11). You can use [wiki:CbuMeg:SensorStats sensor stats] implemented in SPM ([wiki:CbuMeg:SensorSpm SensorSPM]) for statistics in sensor space. |
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3) For [http://imaging.mrc-cbu.cam.ac.uk/meg/SensorSpm SensorSPM] ([http://imaging.mrc-cbu.cam.ac.uk/meg/SensorStats sensor stats]), you should [http://imaging.mrc-cbu.cam.ac.uk/meg/InterpolateData interpolate your MEG data] on a [http://imaging.mrc-cbu.cam.ac.uk/meg/StandardSensorArray standard sensory array]. | 3) For [wiki:CbuMeg:SensorSpm SensorSPM] ([http://imaging.mrc-cbu.cam.ac.uk/meg/SensorStats sensor stats]), you should [wiki:CbuMeg:InterpolateData interpolate your MEG data] on a [wiki:CbuMeg:StandardSensorArray standard sensory array]. |
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4) For data exploration or visualisation, you may want to compute [http://imaging.mrc-cbu.cam.ac.uk/meg/GrandMean grand average data in signal space]. | 4) For data exploration or visualisation, you may want to compute [wiki:CbuMeg:GrandMean grand average data in signal space]. |
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5) Applying the inverse operator to [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_singletrial single-trial data] requires some extra processing steps. | 5) Applying the inverse operator to [wiki:CbuMeg:AnalyzingData/MNE_singletrial single-trial data] requires some extra processing steps. |
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6) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_simulation Simulate] your own data in MNE, e.g. to check localisation accuracy for specific ROIs | 6) [wiki:CbuMeg:AnalyzingData/MNE_simulation Simulate] your own data in MNE, e.g. to check localisation accuracy for specific ROIs |
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7) Compute [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_sensitivity Sensitivity Maps] for EEG and MEG configurations | 7) Compute [wiki:CbuMeg:AnalyzingData/MNE_sensitivity Sensitivity Maps] for EEG and MEG configurations |
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8) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_BaselineCorrectSTC Baseline Correction] for source estimates | 8) [wiki:CbuMeg:AnalyzingData/MNE_BaselineCorrectSTC Baseline Correction] for source estimates |
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9) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Vertices2MNI Converting vertex locations] from MNE STC-files to MNI coordinates | 9) [wiki:CbuMeg:AnalyzingData/MNE_Vertices2MNI Converting vertex locations] from MNE STC-files to MNI coordinates |
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10)[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_SampleDataSet The MNE Sample Data Set] (CBU only) | 10)[wiki:CbuMeg:AnalyzingData/MNE_SampleDataSet The MNE Sample Data Set] (CBU only) |
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[http://imaging.mrc-cbu.cam.ac.uk/meg/MEG_Data_Processing MEG Data Processing] | [wiki:CbuMeg:MEG_Data_Processing MEG Data Processing] |
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[http://imaging.mrc-cbu.cam.ac.uk/imaging/DanStructurals Structural Analysis] | [wiki:CbuImaging:DanStructurals Structural Analysis] |
MEG and EEG Data Analysis Using MNE Software
attachment:MNE_title.jpg
Basics
MEG/EEG data analysis in [http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php MNE software] uses information from structural [wiki:ImagingSequences MRI] images, which have to be pre-processed using [http://surfer.nmr.mgh.harvard.edu/ Freesurfer]. You may want to start with the tutorial based on an example data set, as described in the MNE manual ([http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf Version 2.6] or [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.7.pdf Version 2.7]; chapter 12), or look at [http://www.martinos.org/mne/ some example scripts]. Freesurfer is accompanied by extensive [http://surfer.nmr.mgh.harvard.edu/fswiki Freesurfer Wiki pages], containing a [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide Getting Started] and [http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ FAQ] section. You will need some experience with Linux commands and scripting, which you may find on our [wiki:meg:Beginners beginners' pages].
If you've never used shell scripts before, this [wiki:AnalyzingData/Primer_ShellScripting primer on shell scripting] will get you on the way.
There is also a short description on how to [wiki:AnalyzingData/MNE_prepare prepare for MNE analysis and access the Matlab toolbox].
Look here for [http://mne-tools.github.com/mne-python-intro/ MNE Python tools], e.g. for time-frequency analysis and sensor-space statistics.
The parameters in the following examples are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the MNE manual ([http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf V2.6], [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.7.pdf V 2.7]), [wiki:MEGpapers reading papers], and [wiki:ImagersInterestGroup discussions] with more experienced researchers. You may also want to subscribe to the [http://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis MNE mailing list].
Step-by-step Guide
Note that some of these steps can be done in parallel, for example MRI preprocessing and MEG averaging.
1) [wiki:AnalyzingData/MNE_MRI_preprocessing Pre-process your MRI Data Using Freesurfer]
2) [wiki:AnalyzingData/MNE_MRI_processing Create Source Space and Head Surfaces] (incl. aligning coordinate systems)
3) [wiki:AnalyzingData/MNE_ForwardSolution Compute the Forward Solution and BEM]
4) [wiki:AnalyzingData/MNE_CovarianceMatrix Compute the Noise Covariance Matrix]
5) [wiki:AnalyzingData/MNE_InverseOperator Compute the Inverse Operator]
6) [wiki:AnalyzingData/MNE_Averaging Averaging MEG data] (incl. correcting EEG location information, Marking bad channels)
7) [wiki:AnalyzingData/MNE_ComputeEstimates Compute the Source Estimates] (incl. average cortical surface, grand-averaging)
8) [wiki:AnalyzingData/MNE_Labels ROI/Label analysis] (incl. pre-defined labels, make-your-own)
All-in-One
[wiki:AnalyzingData/MNE_AllInOne List of Most Relevant MNE Commands]
Related Issues
1) You may want to [wiki:PreProcessing filter] or [wiki:Maxfilter maxfilter] ([wiki:MaxfilterMatlabScript Matlab script]) your data before averaging
2) At the moment, MNE does not provide any statistics tools (but see MNE-Python tools, point 11). You can use [wiki:SensorStats sensor stats] implemented in SPM ([wiki:SensorSpm SensorSPM]) for statistics in sensor space.
3) For [wiki:SensorSpm SensorSPM] ([http://imaging.mrc-cbu.cam.ac.uk/meg/SensorStats sensor stats]), you should [wiki:InterpolateData interpolate your MEG data] on a [wiki:StandardSensorArray standard sensory array].
4) For data exploration or visualisation, you may want to compute [wiki:GrandMean grand average data in signal space].
5) Applying the inverse operator to [wiki:AnalyzingData/MNE_singletrial single-trial data] requires some extra processing steps.
6) [wiki:AnalyzingData/MNE_simulation Simulate] your own data in MNE, e.g. to check localisation accuracy for specific ROIs
7) Compute [wiki:AnalyzingData/MNE_sensitivity Sensitivity Maps] for EEG and MEG configurations
8) [wiki:AnalyzingData/MNE_BaselineCorrectSTC Baseline Correction] for source estimates
9) [wiki:AnalyzingData/MNE_Vertices2MNI Converting vertex locations] from MNE STC-files to MNI coordinates
10)[wiki:AnalyzingData/MNE_SampleDataSet The MNE Sample Data Set] (CBU only)
11) [http://mne-tools.github.com/mne-python-intro/ MNE Python tools] and [https://martinos.org/mne/auto_examples/ example scripts] (e.g. averaging, time-frequency analysis, non-parametric statistics)
Dan's Pages (from Martinos Center for Biomedical Imaging)
[wiki:MEG_Data_Processing MEG Data Processing]
[wiki:DanStructurals Structural Analysis]