Basics
[http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php MNE] data analysis uses information from structural 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). 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].
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.
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].
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].
Step-by-step Guide
1) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_preprocessing Pre-process your MRI Data Using Freesurfer]
2) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Create Source Space and Head Surfaces]
3) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution Compute the Forward Solution and BEM]
4) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_CovarianceMatrix Compute the Noise Covariance Matrix]
5) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_InverseOperator Compute the Inverse Operator]
6) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Averaging Averaging MEG data] (incl. correcting EEG location information, Marking bad channels)
7) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Compute the Source Estimates] (incl. average cortical surface, grand-averaging)
8) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Labels ROI/Label analysis] (incl. pre-defined labels, make-your-own)
All-in-One
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_AllInOne List of Most Relevant MNE Commands]
Related Issues
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] your data before averaging
2) At the moment, MNE does not provide any statistics tools. You can use the [http://imaging.mrc-cbu.cam.ac.uk/meg/SensorSpm SensorSPM] implemented in SPM for statistics in sensor space.
Dan's Pages (from Martinos Center for Biomedical Imaging)
[http://imaging.mrc-cbu.cam.ac.uk/meg/MEG_Data_Processing MEG Data Processing]
[http://imaging.mrc-cbu.cam.ac.uk/imaging/DanStructurals Structural Analysis]