This document describes a set of programs for preprocessing and averaging of MEG and EEG data and for constructing cortically-constrained minimum-norm estimates. This software package will in the sequel be referred to as MNE software. The software is based on anatomical MRI processing, forward modeling, and source estimation methods published in Dale, Fischl, Hämäläinen, and others. The software depends on anatomical MRI processing tools provided by the FreeSurfer software.
Overview gives an overview of the software modules included with MNE software. The Cookbook is a concise cookbook describing a typical workflow for a novice user employing the convenience scripts as far as possible. Processing raw data to Miscellaneous utilities give more detailed information about the software modules. The sample data set discusses processing of the sample data set included with the MNE software. Related publications lists some useful background material for the methods employed in the MNE software.
Creating the BEM meshes is an overview of the BEM model mesh generation methods, Setup at the Martinos Center contains information specific to the setup at Martinos Center of Biomedical Imaging, Installation and configuration is a software installation and configuration guide, Release notes summarizes the software history, and Licence agreement contains the End-User License Agreement.
Note
The most recent version of this manual is available at $MNE_ROOT/share/doc/MNE-manual- <version> .pdf . For the present manual, <version> = 2.7 . For definition of the MNE_ROOT environment variable, see User environment.
We want to thank all MNE Software users at the Martinos Center and in other institutions for their collaboration during the creation of this software as well as for useful comments on the software and its documentation.
The development of this software has been supported by the NCRR Center for Functional Neuroimaging Technologies P41RR14075-06, the NIH grants 1R01EB009048-01, R01 EB006385-A101, 1R01 HD40712-A1, 1R01 NS44319-01, and 2R01 NS37462-05, ell as by Department of Energy under Award Number DE-FG02-99ER62764 to The MIND Institute.