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= MEG and EEG Data Analysis Using MNE Software =
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== Basics ==
MEG/EEG data analysis in [[http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php|MNE software]] uses information from structural [[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  ([[attachment:MNE_V2.6.pdf|Version 2.6]], [[attachment:MNE_V2.7.pdf|Version 2.7.1]]; [[attachment:MNE_V2.7.3.pdf|Version 2.7.3]]; 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 [[meg:Beginners|beginners' pages]].

If you've never used shell scripts before, this [[AnalyzingData/Primer_ShellScripting|primer on shell scripting]] will get you on the way.

There is also a short description on how to [[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]]), [[MEGpapers|and reading papers]].

== Step-by-step Guide ==
Note that some of these steps can be done in parallel, for example MRI preprocessing and MEG averaging.

1) [[AnalyzingData/MNE_MRI_preprocessing|Pre-process your MRI Data Using Freesurfer]]

2) [[AnalyzingData/MNE_FixingFIFF|Fix EEG electrode positions in Fiff-files]]

3) [[AnalyzingData/MNE_MRI_processing|Create Source Space and Head Surfaces]] (incl. aligning coordinate systems)

4) [[AnalyzingData/MNE_ForwardSolution|Compute the Forward Solution and BEM]]

5) [[AnalyzingData/MNE_CovarianceMatrix|Compute the Noise Covariance Matrix]]

6) [[AnalyzingData/MNE_InverseOperator|Compute the Inverse Operator]]

7) [[AnalyzingData/MNE_Averaging|Averaging MEG data]] (incl. correcting EEG location information, Marking bad channels)

8) [[AnalyzingData/MNE_ComputeEstimates|Compute the Source Estimates]] (incl. average cortical surface, grand-averaging)

9) [[AnalyzingData/MNE_Labels|ROI/Label analysis]] (incl. pre-defined labels, make-your-own)

== All-in-One ==
[[AnalyzingData/MNE_AllInOne|List of Most Relevant MNE Commands]]

== Related Issues ==
1) You may want to [[PreProcessing|filter]] or [[Maxfilter|maxfilter]] ([[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 [[SensorStats|sensor stats]] implemented in SPM ([[SensorSpm|SensorSPM]]) for statistics in sensor space.

3) For [[SensorSpm|SensorSPM]] ([[http://imaging.mrc-cbu.cam.ac.uk/meg/SensorStats|sensor stats]]), you should [[InterpolateData|interpolate your MEG data]] on a [[StandardSensorArray|standard sensory array]].

4) For data exploration or visualisation, you may want to compute [[GrandMean|grand average data in signal space]].

5) Applying the inverse operator to [[AnalyzingData/MNE_singletrial|single-trial data]] requires some extra processing steps.

6) [[AnalyzingData/MNE_simulation|Simulate]] your own data in MNE, e.g. to check localisation accuracy for specific ROIs

7) Compute [[AnalyzingData/MNE_sensitivity|Sensitivity Maps]] for EEG and MEG configurations

8) [[AnalyzingData/MNE_BaselineCorrectSTC|Baseline Correction]] for source estimates

9) [[AnalyzingData/MNE_Vertices2MNI|Converting vertex locations]] from MNE STC-files to MNI coordinates

10)[[AnalyzingData/MNE_SampleDataSet|The MNE Sample Data Set]] (CBU only)

11) [[AnalyzingData/MNE_Python_CBU|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) ==
[[MEG_Data_Processing|MEG Data Processing]]

[[CbuImaging:DanStructurals|Structural Analysis]]