MNE-CPP Manual

Overview

MNE-CPP provides a comprehensive set of tools for preprocessing and averaging of MEG and EEG data and for constructing cortically-constrained minimum-norm estimates. The software is based on anatomical MRI processing, forward modelling, and source estimation methods. The anatomical MRI processing routines depend on tools provided by the FreeSurfer software.

This manual gives an overview of the software modules included with MNE-CPP, describes a typical workflow for a novice user, and provides detailed information about the individual software modules.

Heritage

MNE-CPP is a C++ port of the original MNE software suite created by Matti Hämäläinen at the Martinos Center for Biomedical Imaging. This manual is adapted from the original MNE Manual and the MNE-Python documentation, preserving the valuable background information and mathematical descriptions while documenting the C++ implementations available in MNE-CPP.

Software Components

The MNE-CPP software suite includes the following main components:

GUI Applications

Application	Description
mne_scan	Real-time acquisition and processing of MEG/EEG data with plugin-based architecture
mne_analyze	Sensor- and source-level analysis of pre-recorded MEG/EEG data (under development)
mne_anonymize	Removes or modifies personal health information from FIFF files (GUI and CLI)
mne_inspect	3D brain visualization and source analysis
mne_browse	Browsing and visualization of raw MEG/EEG FIFF data files (under development)

Command-Line Tools

Tool	Description
mne_compute_raw_inverse	Computes inverse solutions (MNE/dSPM/sLORETA) from raw or evoked data
mne_dipole_fit	Performs electric current dipole fitting on MEG/EEG data
mne_edf2fiff	Converts EDF (European Data Format) files to FIFF format
mne_forward_solution	Computes the MEG/EEG forward solution
mne_show_fiff	Lists the contents of a FIFF file
mne_flash_bem	Creates BEM surfaces using multi-echo FLASH MRI sequences
mne_setup_forward_model	Sets up the BEM for forward modeling
mne_setup_mri	Sets up FreeSurfer MRI data for MNE processing
mne_surf2bem	Converts FreeSurfer surfaces to BEM FIFF files
mne_watershed_bem	Creates BEM surfaces using FreeSurfer's watershed algorithm
mne_rt_server	Real-time FIFF data streaming server

Prerequisites

To make full use of the MNE-CPP software, you will need:

• FreeSurfer: Required for anatomical MRI processing, cortical surface reconstruction, and the creation of BEM meshes. Available at https://surfer.nmr.mgh.harvard.edu/.

• MEG/EEG Data: Data in FIFF format (the native format of Neuromag/Elekta/MEGIN MEG systems). Data from other systems can be converted using appropriate tools (e.g., mne_edf2fiff for EDF data).

• Environment Variables: Several MNE-CPP tools rely on the following environment variables:

  • SUBJECTS_DIR — The directory containing FreeSurfer subject reconstructions
  • SUBJECT — The name of the current subject
  • FREESURFER_HOME — The FreeSurfer installation directory

Chapter Overview

• The Typical MEG/EEG Workflow — A step-by-step guide through a typical analysis pipeline
• The Forward Solution — Coordinate systems, BEM models, and forward computation
• The Minimum-Norm Estimates — Mathematical background of inverse estimation methods
• Signal-Space Projection — The SSP method for noise rejection
• Command-Line Tools Reference — Detailed reference for all command-line tools
• MNE Browse Raw — The raw data browser application
• MNE Analyze — The analysis and visualization application

Acknowledgments

The development of the MNE software has been supported by the National Center for Research Resources (NCRR), the NIH (grants R01EB009048, R01EB006385, R01HD40712), and the U.S. Department of Energy. We are grateful to the MNE software users at the Martinos Center and other institutions for their collaboration and valuable feedback on the software and its documentation.