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References to implemented methods

This page links to the original publications that describe the methods implemented in the FieldTrip toolbox. If you are looking for specific implementation details, please look at the reference documentation.

This list is far from complete, FieldTrip implements many more algorithms that have been published in papers. If you want to know which paper describes a method in detail and the information is not given here, you can ask on the email discussion list.

If you know of references to original work that is not listed here, please send a pull request to add them here. When possible, please provide a link to the online version of the manuscript. A link to pubmed or sciencedirect is nice, as it allows quick cross-referencing. You can also link to the digital object identifier or to an online pdf version.

EEG and MEG forward modeling

Forward model solution for MEG, single homogenous sphere

Cuffin BN, Cohen D. Magnetic fields of a dipole in special volume conductor shapes. IEEE Trans Biomed Eng. 1977 Jul;24(4):372-81.

Forward model solution for MEG, multiple sphere

Huang MX, Mosher JC, Leahy RM. A sensor-weighted overlapping-sphere head model and exhaustive head model comparison for MEG. Phys Med Biol. 1999 Feb;44(2):423-40.

Forward model solution for MEG, realistic single shell

Nolte G. The magnetic lead field theorem in the quasi-static approximation and its use for magnetoencephalography forward calculation in realistic volume conductors. Phys Med Biol. 2003 Nov 21;48(22):3637-52.

Forward model solution for EEG, single homogenous and isotropic sphere

Kavanagh R, Darcey TM, Lehmann D, Fender DH. Evaluation of methods for three-dimensional localization of electric sources in the human brain. IEEE Trans Biomed Eng. 1978;25:421-9.

Forward model solution for EEG, inhomogenous concentric 4-sphere model

Cuffin BN, Cohen D. Comparison of the magnetoencephalogram and electroencephalogram. Electroencephalogr Clin Neurophysiol. 1979 Aug;47(2):132-46.

Forward model solution for EEG, using BEM

Fuchs M, Kastner J, Wagner M, Hawes S, Ebersole JS. A standardized boundary element method volume conductor model. Clin Neurophysiol. 2002 May;113(5):702-12.

Oostendorp T, van Oosterom A. The potential distribution generated by surface electrodes in inhomogeneous volume conductors of arbitrary shape. IEEE Trans Biomed Eng. 1991 May;38(5):409-17.

Forward model solution for EEG, using FEM

Vorwerk J, Oostenveld R, Piastra MC, Magyari L, Wolters CH. The FieldTrip-SimBio pipeline for EEG forward solutions. BioMed Eng OnLine. 2018;17:37.

Vorwerk J, Cho JH, Rampp S, Hamer H, Knösche TR, Wolters CH. A guideline for head volume conductor modeling in EEG and MEG. Neuroimage. 2014;100:590-607.

Vorwerk J, Clerc M, Burger M, Wolters CH. Comparison of boundary element and finite element approaches to the EEG forward problem. Biomed Tech (Berl). 2012;57(Suppl 1):795-8.

EEG and MEG source estimation

Beamformer source analysis in the time-domain using LCMV

Van Veen BD, van Drongelen W, Yuchtman M, Suzuki A. Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Trans Biomed Eng. 1997 Sep;44(9):867-80.

Beamformer source analysis in the frequency-domain using DICS

Gross J, Kujala J, Hämäläinen M, Timmermann L, Schnitzler A, Salmelin R. Dynamic imaging of coherent sources: studying neural interactions in the human brain. Proc Natl Acad Sci USA. 2001 Jan 16;98(2):694-9.

Source localization by fitting an equivalent current dipole model

Scherg M. Fundamentals of dipole source potential analysis. In: Grandori F, Hoke M, Romani GL, editors. Auditory evoked magnetic fields and electric potentials. Basel: Karger; 1990. p. 40-69. (Advances in audiology; vol. 6).

Distributed source reconstruction using linear estimation

Dale AM, Liu AK, Fischl B, Buckner RL, Belliveau JW, Lewine JD, et al. Dynamic statistical parametric mapping: combining fMRI and MEG to produce high-resolution spatiotemporal maps of cortical activity. Neuron. 2000;26:55-67.

Liu AK, Dale AM, Belliveau JW. Monte Carlo simulation studies of EEG and MEG localization accuracy. Hum Brain Mapp. 2002;16:47-62.

Lin FH, Witzel T, Hämäläinen MS, Dale AM, Belliveau JW, Stufflebeam SM. Spectral spatiotemporal imaging of cortical oscillations and interactions in the human brain. Neuroimage. 2004;23:582-95.

Using multiple signal classification (MUSIC) to scan the source space

Mosher JC, Lewis PS, Leahy RM. Multiple dipole modeling and localization from spatio-temporal MEG data. IEEE Trans Biomed Eng. 1992 Jun;39(6):541-57.

Mosher JC, Baillet S, Leahy RM. EEG source localization and imaging using multiple signal classification approaches. J Clin Neurophysiol. 1999 May;16(3):225-38.

Frequency analysis

Smoothing in the frequency domain with multiple Slepian tapers

Mitra PP, Pesaran B. Analysis of dynamic brain imaging data. Biophys J. 1999 Feb;76(2):691-708.

Jarvis MR, Mitra PP. Sampling properties of the spectrum and coherency of sequences of action potentials. Neural Comput. 2001 Apr;13(4):717-49.

Convolution in the time-domain with Morlet’s wavelets

Tallon-Baudry C, Bertrand O, Delpuech C, Permier J. Oscillatory gamma-band (30-70 Hz) activity induced by a visual search task in humans. J Neurosci. 1997 Jan 15;17(2):722-34.

Irregular-resampling auto-spectral analysis (IRASA)

Wen H, Liu Z. Separating fractal and oscillatory components in the power spectrum of neurophysiological signal. Brain Topogr. 2016 Jan;29(1):13-26.

On the differences and similarities between short-time Fourier, wavelet, and Hilbert transform

Bruns A. Fourier-, Hilbert- and wavelet-based signal analysis: are they really different approaches? J Neurosci Methods. 2004 Aug 30;137(2):321-32.

Dealing with different head positions and with movements

Knosche TR. Transformation of whole-head MEG recordings between different sensor positions. Biomed Tech (Berl). 2002 Mar;47(3):59-62.

Stolk A, Todorovic A, Schoffelen JM, Oostenveld R. Online and offline tools for head movement compensation in MEG. Neuroimage. 2013;68:39-48.

Scalp current density mapping

Oostendorp TF, van Oosterom A. The surface Laplacian of the potential: theory and application. IEEE Trans Biomed Eng. 1996 Apr;43(4):394-405.

Perrin F, Pernier J, Bertrand O, Echallier JF. Spherical splines for scalp potential and current density mapping. Electroencephalogr Clin Neurophysiol. 1989;72:184-7.

Planar gradient computation

Bastiaansen MCM, Knösche TR. MEG tangential derivative mapping applied to event-related desynchronization (ERD) research. Clin Neurophysiol. 2000;111:1300-5.

Connectivity analysis

General tutorial + some things to think about

Bastos AM, Schoffelen JM. A tutorial review of functional connectivity analysis methods and their interpretational pitfalls. Front Syst Neurosci. 2016;9:175.

Coherence

Rosenberg JR, Amjad AM, Breeze P, Brillinger DR, Halliday DM. The Fourier approach to the identification of functional coupling between neuronal spike trains. Prog Biophys Mol Biol. 1989;53:1-31.

Phase locking value

Lachaux JP, Rodriguez E, Martinerie J, Varela FJ. Measuring phase synchrony in brain signals. Hum Brain Mapp. 1999;8:194-208.

Partial coherence

Rosenberg JR, Halliday DM, Breeze P, Conway BA. Identification of patterns of neuronal connectivity - partial spectra, partial coherence, and neuronal interactions. J Neurosci Methods. 1998;83:57-72.

Imaginary part of coherency

Nolte G, Bai O, Wheaton L, Mari Z, Vorbach S, Hallett M. Identifying true brain interaction from EEG data using the imaginary part of coherence. Clin Neurophysiol. 2004;115:2292-307.

Phase slope index

Nolte G, Ziehe A, Nikulin VV, Schlögl A, Krämer N, Brismar T, et al. Robustly estimating the flow direction of information in complex physical systems. Phys Rev Lett. 2008;100:234101.

Partial directed coherence

Baccalá LA, Sameshima K. Partial directed coherence: a new concept in neural structure determination. Biol Cybern. 2001;84:463-74.

Directed transfer function

Kamiński MJ, Blinowska KJ. A new method of the description of the information flow in the brain structures. Biol Cybern. 1991;65:203-10.

Spectrally resolved Granger causality

Ding M, Chen Y, Bressler SL. Granger causality: basic theory and application to neuroscience. In: Schelter B, Winterhalder M, Timmer J, editors. Handbook of time series analysis. Weinheim: Wiley-VCH; 2006. p. 451-74. arXiv:q-bio/0608035.

Dhamala M, Rangarajan G, Ding M. Analyzing information flow in brain networks with nonparametric Granger causality. Neuroimage. 2008 Jun;41(2):354-62.

Dhamala M, Rangarajan G, Ding M. Estimating Granger causality from Fourier and wavelet transforms of time series data. Phys Rev Lett. 2008 Jan 11;100(1):018701.

Pairwise Phase Consistency

Vinck M, van Wingerden M, Womelsdorf T, Fries P, Pennartz CMA. The pairwise phase consistency: a bias-free measure of rhythmic neuronal synchronization. Neuroimage. 2010 May 15;51(1):112-22.

Weighted Phase Lag Index

Vinck M, Oostenveld R, van Wingerden M, Battaglia F, Pennartz CMA. An improved index of phase-synchronization for electrophysiological data in the presence of volume-conduction, noise and sample-size bias. Neuroimage. 2011 Apr 15;55(4):1548-65.

Spike-LFP phase-coupling measures

Vinck M, Battaglia FP, Womelsdorf T, Pennartz CMA. Improved measures of phase-coupling between spikes and the local field potential. J Comput Neurosci. 2012;33:53-75.

Statistics for EEG- and MEG-data

Maris E. Statistical testing in electrophysiological studies. Psychophysiology. 2012;49(4):549-65.

Statistical inference by means of permutation

Maris E, Oostenveld R. Nonparametric statistical testing of EEG- and MEG-data. J Neurosci Methods. 2007;164(1):177-90.

Maris E, Schoffelen JM, Fries P. Nonparametric statistical testing of coherence differences. J Neurosci Methods. 2007 Jun 15;163(1):161-75.

Multiple comparison corrections

Holm S. A simple sequentially rejective multiple test procedure. Scand J Stat. 1979;6(2):65-70.

Hochberg Y. A sharper Bonferroni procedure for multiple tests of significance. Biometrika. 1988;75(4):800-2.

Genovese CR, Lazar NA, Nichols T. Thresholding of statistical maps in functional neuroimaging using the false discovery rate. Neuroimage. 2002;15(4):870-8.

Machine learning

van Gerven MAJ, Hesse C, Jensen O, Heskes T. Interpreting single trial data using groupwise regularisation. Neuroimage. 2009;46(3):665-76.

Brain-computer interfacing

van Gerven MAJ, Jensen O. Attention modulations of posterior alpha as a control signal for two-dimensional brain-computer interfaces. J Neurosci Methods. 2009;179:78-84.

Intracranial EEG analysis

Stolk A, Griffin S, van der Meij R, Dewar C, Saez I, Piantoni G, et al. Integrated analysis of anatomical and electrophysiological human intracranial data. Nat Protoc. 2018;13(7):1699-723.

Mercier MR, Dubarry AS, Tadel F, Avanzini P, Axmacher N, Cellier D, et al. Advances in human intracranial electroencephalography research, guidelines and good practices. Neuroimage. 2022;260:119438.