AnalyzingData/MNE_overview - Meg Wiki

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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 [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf MNE manual] (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.

If you want to use the MNE Matlab toolbox on a regular basis, you should add the line

  • run /imaging/local/linux/mne_2.6.0/mne/matlab/toolbox/mne_setup_toolbox.m

to your startup.m file. If you run mne_setup_2.6.0 before starting Matlab, it will automatically add the paths to the MNE tools.

The parameters in the following examples are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf MNE manual], [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].

Overview of MNE Analysis Path at CBU

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 Compute the Averages]

7) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Compute the Source Estimates] (average cortical surface, grand-averaging)

8) [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Labels ROI/Label analysis]

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]