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References to implemented methods |
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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 references 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 to this page. When possible, please provide a link to the online version of the manuscript. A link to pubmed or sciencedirect is in general nice, as it allows quick cross-referencing. You can also link to an online pdf version of the manuscript.
Please check Sherpa Romeo for the copyright conditions and whether you are allowed to
- release the publisher version, i.e. the final online pdf version from Elsevier or so
- release a self-archived version, i.e. your own pdf (or word) document as it has been accepted for publication
- not release a copy of the manuscript that is freely available to everyone
Cuffin BN, Cohen D. Magnetic fields of a dipole in special volume conductor shapes. IEEE Trans Biomed Eng. 1977 Jul;24(4):372-81.
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.
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
R. Kavanagh, T. M. Darccey, D. Lehmann, and D. H. Fender. Evaluation of methods for three-dimensional localization of electric sources in the human brain. IEEE Trans Biomed Eng, 25:421-429, 1978.
Cuffin BN, Cohen D. Comparison of the magnetoencephalogram and electroencephalogram. Electroencephalogr Clin Neurophysiol. 1979 Aug;47(2):132-46.
Fuchs M, Kastner J, Wagner M, Hawes S, Ebersole J.S. 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.
Vorwerk, J., Oostenveld, R., Piastra M.C., Magyari, L. & Wolters, C. H. The FieldTripSimBio pipeline for EEG forward solutions. BioMed Eng OnLine (2018) 17:37. DOI: 10.1186/s12938-018-0463-y.
Vorwerk, J., Cho, J.-H., Rampp, S., Hamer, H., Knosche, T.R., Wolters, C.H., A Guideline for Head Volume Conductor Modeling in EEG and MEG. NeuroImage, 100, pp.590-607, (2014).
Vorwerk, J., Clerc, M., Burger, M. and Wolters, C.H., Comparison of Boundary Element and Finite Element Approaches to the EEG Forward Problem. Biomedical Engineering, 57(Suppl.1), pp.795-798, doi:10.1515/bmt-2012-4152, (2012).
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.
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.
Scherg M. Fundamentals of dipole source potential analysis. In: Auditory evoked magnetic fields and electric potentials. eds. F. Grandori, M. Hoke and G.L. Romani. Advances in Audiology, vol. 6. Karger, Basel, pp 40-69, 1990.
Dale AM, Liu AK, Fischl B, Buckner RL, Belliveau JW, Lewine JD, Halgren E (2000): Dynamic statistical parametric mapping: combining fMRI and MEG to produce high-resolution spatiotemporal maps of cortical activity. Neuron 26:55-67.
Arthur K. Liu, Anders M. Dale, and John W. Belliveau (2002): Monte Carlo Simulation Studies of EEG and MEG Localization Accuracy. Human Brain Mapping 16:47-62.
Fa-Hsuan Lin, Thomas Witzel, Matti S. Hämäläinen, Anders M. Dale, John W. Belliveau, and Steven M. Stufflebeam (2004): Spectral spatiotemporal imaging of cortical oscillations and interactions in the human brain. NeuroImage 23:582-595.
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.
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.
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.
Wen H, Liu Z. Separating fractal and oscillatory components in the power spectrum of neurophysiological signal. Brain Topogr. 2016 Jan;29(1):13-26.
Bruns A, Fourier-, Hilbert-and wavelet-based signal analysis: are they really different approaches?. J.Neurosci.Meth. 2004 Aug;137(2):321-332
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 J-M, Oostenveld R. Online and offline tools for head movement compensation in MEG. NeuroImage. 2013.
TF Oostendorp, A van Oosterom. The surface Laplacian of the potential: theory and application. IEEE Trans Biomed Eng, 43(4): 394-405, 1996.
F. Perrin, J. Pernier, O. Bertrand, and J. F. Echallier. Spherical splines for scalp potential and current density mapping. Electroencephalogr Clin Neurophysiol, 72:184-187, 1989.
Bastiaansen, M. C. M., & Knsche, T. R. (2000). MEG tangential derivative mapping applied to Event-Related Desynchronization (ERD) research. Clinical Neurophysiology, 111, 1300-1305.
Bastos and Schoffelen A Tutorial Review of Functional Connectivity Analysis Methods and Their Interpretational Pitfalls Front. Syst. Neurosci., 08 January 2016.
Rosenberg et al. The Fourier approach to the identification of functional coupling between neuronal spike trains. Prog Biophys Molec Biol 1989; 53; 1-31
Lachaux et al. Measuring phase synchrony in brain signals. Human Brain Mapping, 1999; 8; 194-208
Rosenberg et al. Identification of patterns of neuronal connectivity - partial spectra, partial coherence, and neuronal interactions. J. Neurosci. Methods, 1998; 83; 57-72
Nolte et al. Identifying true brain interaction from EEG data using the imaginary part of coherence. Clinical Neurophysiology, 2004; 115; 2292-2307
Nolte et al. Robustly estimating the flow direction of information in complex physical systems. Physical Review Letters, 2008; 100; 234101
Baccala and Sameshima. Partial directed coherence: a new concept in neural structure determination. Biol. Cybern., 2001; 84; 463-474
Kaminski and Blinowska. A new method of the description of the information flow in the brain structures. Biol. Cybern., 1991; 65; 203-210
Mingzhou Ding, Yonghong Chen, Steven L. Bressler. Granger Causality: Basic Theory and Application to Neuroscience. In: Handbook of Time Series Analysis, ed. B. Schelter, M. Winterhalder, and J. Timmer, Wiley-VCH Verlage, 2006: 451-474. arXiv:q-bio/0608035v1
Dhamala M, Rangarajan G, Ding M. Analyzing information flow in brain networks with nonparametric Granger causality. Neuroimage. 2008 Jun;41(2):354-62. Epub 2008 Feb 25. PubMed PMID: 18394927; PubMed Central PMCID: PMC2685256.
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. Epub 2008 Jan 10. PubMed PMID: 18232831.
Vinck M, van Wingerden M, Womelsdorf T, Fries P, Pennartz CM. The pairwise phase consistency: a bias-free measure of rhythmic neuronal synchronization. Neuroimage. 2010 May 15;51(1):112-22. Epub 2010 Jan 28. PMID: 20114076
Vinck M, Oostenveld R, van Wingerden M, Battaglia F, Pennartz CM. 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. Epub 2011 Jan 27. PMID: 21276857
Vinck, M, Battaglia FP, Womelsdorf T, Pennartz CM. Improved measures of phase-coupling between spikes and the Local Field Potential. 2011; DOI: 10.1007/s10827-011-0374-4
Maris E. Statistical Testing in Electrophysiological Studies Psychophysiology (2012) Vol 49 No 4, pp. 549-65.
Maris E., Oostenveld R. Nonparametric statistical testing of EEG- and MEG-data. J Neurosci Methods. 2007 Apr 10;
Maris E., Schoffelen J.M., Fries P. Nonparametric statistical testing of coherence differences. J Neurosci Methods. 2007 Jun 15;163(1):161-75.
Holm S. A Simple Sequentially Rejective Multiple Test Procedure. Scandinavian Journal of Statistics, Vol. 6, No. 2 (1979), pp. 65-70.
Hochberg Y. A Sharper Bonferroni Procedure for Multiple Tests of Significance Biometrika Vol. 75 No. 4 (1988), pp. 800802.
Genovese C.R., Lazar N.A., Nichols T. Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate Neuroimage Vol. 15 No. 4 (2002), pp. 870-8.
Van Gerven, M.A.J., Hesse, C., Jensen, O., Heskes, T. Interpreting Single Trial Data using Groupwise Regularisation. Neuroimage. 2009; 46(3):665-76.
Van Gerven, M.A.J., Jensen, O. Attention Modulations of Posterior Alpha as a Control Signal for Two-Dimensional Brain-Computer Interfaces. J Neurosci Methods. 2009; 179:78-84.
Stolk A., Griffin S., van der Meij R., Dewar C., Saez I., Piantoni G., Schoffelen J.M., Knight R.T., Oostenveld R. Integrated Analysis of Anatomical and Electrophysiological Human Intracranial Data. Nature Protocols. 2018; 13(7):1699-1723