Hindawi Publishing Corporation Computational Intelligence and Neuroscience Volume 2011, Article ID 156869, 9 pages doi:10.1155/2011/156869 Research Article FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data Robert Oostenveld, 1 Pascal Fries, 1, 2 Eric Maris, 1 and Jan-Mathijs Schoffelen 1 1 Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands 2 Ernst Str¨ ungmann Institute and Max Planck Society, D-60528 Frankfurt, Germany Correspondence should be addressed to Robert Oostenveld, r.oostenveld@donders.ru.nl Received 26 August 2010; Accepted 18 October 2010 Academic Editor: Sylvain Baillet Copyright © 2011 Robert Oostenveld et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user- friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages. 1. General Overview FieldTrip is a MATLAB-toolbox for the analysis of MEG, EEG, and other electrophysiological data, which is freely available from http://www.ru.nl/neuroimaging/fieldtrip un- der the GNU public license. The development of FieldTrip started in 2003 at the F.C. Donders Centre for Cognitive Neuroimaging and up to today it continues to be actively developed at the Donders Institute for Brain, Cognition and Behaviour of the Radboud University Nijmegen, the Netherlands, together with collaborating researchers and institutes. The software is fully implemented in MATLAB, a high- level technical computing language and interactive environ- ment for algorithm development, data analysis, and visual- ization, which is available for all commonly used computer platforms (http://www.mathworks.com). MATLAB is widely known and used in the neuroimaging community. Although MATLAB is relatively expensive, the investment is easily compensated by the rich feature set and flexibility it provides. The FieldTrip toolbox consists of approximately 108 high-level and 858 low-level functions with in total 103227 lines of code. The main focus is on the analysis of nonin- vasive and invasive electrophysiological data, including spike recordings, but in theory any time series data (e.g., BOLD or NIRS time courses) can be analysed. The toolbox supports reading data from a large number of different file formats (Table 1). Supported functionality includes algorithms for data preprocessing, event-related field/response analysis, parametric and nonparametric spectral analysis, forward and inverse source modelling, connectivity analysis, classi- fication, real-time data processing, and statistical inference. Finally, the toolbox contains a module allowing for peer- to-peer distributed computing. The structure of the toolbox with its modules is shown schematically in Figure 1. An important goal of the FieldTrip project is to provide a common platform for experimental scientists and meth- ods developers. The FieldTrip toolbox allows experimental scientists to have access to state-of-the-art data analysis algo- rithms. For methods developers it facilitates their algorithms to be applied to a large variety of experimental data. The organization of the FieldTrip project facilitates a highly dynamic development model with a rapid availability of software updates to the user. This is realized by a daily