Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne.

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MEG and EEG data analysis with MNE-Python

MNE software for processing MEG and EEG data

Oscillatory neuronal activity may provide a mechanism for dynamic network coordination. Rhythmic neuronal interactions can be quantified using multiple metrics, each with their own advantages and disadvantages. This tutorial will review and summarize current analysis methods used in the field of invasive and non-invasive electrophysiology to study the dynamic connections between neuronal populations. First, we review metrics for functional connectivity, including coherence, phase synchronization, phase-slope index, and Granger causality, with the specific aim to provide an intuition for how these metrics work, as well as their quantitative definition. Next, we highlight a number of interpretational caveats and common pitfalls that can arise when performing functional connectivity analysis, including the common reference problem, the signal to noise ratio problem, the volume conduction problem, the common input problem, and the trial sample size bias problem. These pitfalls will be illustrated by presenting a set of MATLAB-scripts, which can be executed by the reader to simulate each of these potential problems. We discuss of how these issues can be addressed using current methods.

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A Tutorial Review of Functional Connectivity Analysis Methods and Their Interpretational Pitfalls

This paper describes the OpenViBE software platform which enables researchers to design, test, and use brain--computer interfaces (BCIs). BCIs are communication systems that enable users to send commands to computers solely by means of brain activity. BCIs are gaining interest among the virtual reality (VR) community since they have appeared as promising interaction devices for virtual environments (VEs). The key features of the platform are (1) high modularity, (2) embedded tools for visualization and feedback based on VR and 3D displays, (3) BCI design made available to non-programmers thanks to visual programming, and (4) various tools offered to the different types of users. The platform features are illustrated in this paper with two entertaining VR applications based on a BCI. In the first one, users can move a virtual ball by imagining hand movements, while in the second one, they can control a virtual spaceship using real or imagined foot movements. Online experiments with these applications together with the evaluation of the platform computational performances showed its suitability for the design of VR applications controlled with a BCI. OpenViBE is a free software distributed under an open-source license.

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Openvibe: An open-source software platform to design, test, and use brain--computer interfaces in real and virtual environments

ICLabel: An automated electroencephalographic independent component classifier, dataset, and website.

We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for ComputationalNeuroscience (SCCN) that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1) a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2) a neuroelectromagnetic forward head modeling toolbox (NFT) for building realistic electrical head models from available data; (3) a source information flow toolbox (SIFT) for modeling ongoing or event-related effective connectivity between cortical areas; (4) a BCILAB toolbox for building online brain-computer interface (BCI) models from available data, and (5) an experimental real-time interactive control and analysis (ERICA) environment for real-time production and coordination of interactive, multimodal experiments.

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EEGLAB, SIFT, NFT, BCILAB, and ERICA: new tools for advanced EEG processing

We report the design and performance of a brain-computer interface (BCI) system for real-time single-trial binary classification of viewed images based on participant-specific dynamic brain response signatures in high-density (128-channel) electroencephalographic (EEG) data acquired during a rapid serial visual presentation (RSVP) task. Image clips were selected from a broad area image and presented in rapid succession (12/s) in 4.1-s bursts. Participants indicated by subsequent button press whether or not each burst of images included a target airplane feature. Image clip creation and search path selection were designed to maximize user comfort and maintain user awareness of spatial context. Independent component analysis (ICA) was used to extract a set of independent source time-courses and their minimally-redundant low-dimensional informative features in the time and time-frequency amplitude domains from 128-channel EEG data recorded during clip burst presentations in a training session. The naive Bayes fusion of two Fisher discriminant classifiers, computed from the 100 most discriminative time and time-frequency features, respectively, was used to estimate the likelihood that each clip contained a target feature. This estimator was applied online in a subsequent test session. Across eight training/test session pairs from seven participants, median area under the receiver operator characteristic curve, by tenfold cross validation, was 0.97 for within-session and 0.87 for between-session estimates, and was nearly as high (0.83) for targets presented in bursts that participants mistakenly reported to include no target features.

Brain Activity-Based Image Classification From Rapid Serial Visual Presentation

We first discuss two MATLAB-centered solutions for real-time data streaming, the environments FieldTrip (Donders Institute, Nijmegen) and DataSuite (Data- River, Producer, MatRiver) (Swartz Center, La Jolla). We illustrate the relative simplicity of coding BCI feature extraction and classification under MATLAB (The Mathworks, Inc.) using a minimalist BCI example, and then describe BCILAB (Team PhyPa, Berlin), a new BCI package that uses the data structures and extends the capabilities of the widely used EEGLAB signal processing environment. We finally review the range of standalone and MATLAB-based software currently freely available to BCI researchers.

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Andrey Vankov

Papers

EEGLAB, SIFT, NFT, BCILAB, and ERICA: new tools for advanced EEG processing

Brain Activity-Based Image Classification From Rapid Serial Visual Presentation

MATLAB-Based Tools for BCI Research