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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 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.
Cuffin BN, Cohen D. Magnetic fields of a dipole in special volume conductor shapes. IEEE Trans Biomed Eng. 1977 Jul;24(4):372-81. {% include badge doi="10.1109/TBME.1977.326188" pmid="881208" %}
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. {% include badge doi="10.1088/0031-9155/44/2/010" pmid="10070792" %}
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. {% include badge doi="10.1088/0031-9155/48/22/002" pmid="14680264" %}
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. {% include badge doi="10.1109/TBME.1978.326336" pmid="700711" %}
Cuffin BN, Cohen D. Comparison of the magnetoencephalogram and electroencephalogram. Electroencephalogr Clin Neurophysiol. 1979 Aug;47(2):132-46. {% include badge doi="10.1016/0013-4694(79)90215-7" pmid="95707" %}
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. {% include badge doi="10.1016/S1388-2457(02)00030-5" pmid="11976050" %}
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. {% include badge doi="10.1109/10.81559" pmid="1874522" %}
Vorwerk J, Oostenveld R, Piastra MC, Magyari L, Wolters CH. The FieldTrip-SimBio pipeline for EEG forward solutions. BioMed Eng OnLine. 2018;17:37. {% include badge doi="10.1186/s12938-018-0463-y" pmid="29580236" %}
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. {% include badge doi="10.1016/j.neuroimage.2014.06.040" pmid="24971512" %}
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. {% include badge doi="10.1515/bmt-2012-4152" pmid="23096316" %}
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. {% include badge doi="10.1109/10.623056" pmid="9282479" %}
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. {% include badge doi="10.1073/pnas.98.2.694" pmid="11209067" %}
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).
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. {% include badge doi="10.1016/S0896-6273(00)81138-1" pmid="10898358" %}
Liu AK, Dale AM, Belliveau JW. Monte Carlo simulation studies of EEG and MEG localization accuracy. Hum Brain Mapp. 2002;16:47-62. {% include badge doi="10.1002/hbm.10024" pmid="11870926" %}
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. {% include badge doi="10.1016/j.neuroimage.2004.04.027" pmid="15488405" pmcid="PMC2884198" %}
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. {% include badge doi="10.1109/10.141192" pmid="1601435" %}
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. {% include badge doi="10.1097/00004691-199905000-00004" pmid="10426406" %}
Mitra PP, Pesaran B. Analysis of dynamic brain imaging data. Biophys J. 1999 Feb;76(2):691-708. {% include badge doi="10.1016/S0006-3495(99)77236-X" pmid="9929474" %}
Jarvis MR, Mitra PP. Sampling properties of the spectrum and coherency of sequences of action potentials. Neural Comput. 2001 Apr;13(4):717-49. {% include badge doi="10.1162/089976601300014312" pmid="11255566" %}
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. {% include badge doi="10.1523/JNEUROSCI.17-02-00722.1997" pmid="8987794" %}
Wen H, Liu Z. Separating fractal and oscillatory components in the power spectrum of neurophysiological signal. Brain Topogr. 2016 Jan;29(1):13-26. {% include badge doi="10.1007/s10548-015-0448-5" pmid="26318848" %}
Bruns A. Fourier-, Hilbert- and wavelet-based signal analysis: are they really different approaches? J Neurosci Methods. 2004 Aug 30;137(2):321-32. {% include badge doi="10.1016/j.jneumeth.2004.03.002" pmid="15262077" %}
Knosche TR. Transformation of whole-head MEG recordings between different sensor positions. Biomed Tech (Berl). 2002 Mar;47(3):59-62. {% include badge doi="10.1515/bmte.2002.47.3.59" pmid="11977444" %}
Stolk A, Todorovic A, Schoffelen JM, Oostenveld R. Online and offline tools for head movement compensation in MEG. Neuroimage. 2013;68:39-48. {% include badge doi="10.1016/j.neuroimage.2012.11.047" pmid="23246857" %}
Oostendorp TF, van Oosterom A. The surface Laplacian of the potential: theory and application. IEEE Trans Biomed Eng. 1996 Apr;43(4):394-405. {% include badge doi="10.1109/10.486279" pmid="8626188" %}
Perrin F, Pernier J, Bertrand O, Echallier JF. Spherical splines for scalp potential and current density mapping. Electroencephalogr Clin Neurophysiol. 1989;72:184-7. {% include badge doi="10.1016/0013-4694(89)90180-6" pmid="2464490" %}
Bastiaansen MCM, Knösche TR. MEG tangential derivative mapping applied to event-related desynchronization (ERD) research. Clin Neurophysiol. 2000;111:1300-5. {% include badge doi="10.1016/S1388-2457(00)00318-7" pmid="10880806" %}
Bastos AM, Schoffelen JM. A tutorial review of functional connectivity analysis methods and their interpretational pitfalls. Front Syst Neurosci. 2016;9:175. {% include badge doi="10.3389/fnsys.2015.00175" pmid="26778976" %}
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. {% include badge doi="10.1016/0079-6107(89)90004-7" pmid="2682781" %}
Lachaux JP, Rodriguez E, Martinerie J, Varela FJ. Measuring phase synchrony in brain signals. Hum Brain Mapp. 1999;8:194-208. {% include badge doi="10.1002/(sici)1097-0193(1999)8:4%3C194::aid-hbm4%3E3.0.co;2-c" pmid="10619414" %}
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. {% include badge doi="10.1016/S0165-0270(98)00069-2" pmid="9765051" %}
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. {% include badge doi="10.1016/j.clinph.2004.04.029" pmid="15351371" %}
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. {% include badge doi="10.1103/PhysRevLett.100.234101" pmid="18643502" %}
Baccalá LA, Sameshima K. Partial directed coherence: a new concept in neural structure determination. Biol Cybern. 2001;84:463-74. {% include badge doi="10.1007/PL00007990" pmid="11417058" %}
Kamiński MJ, Blinowska KJ. A new method of the description of the information flow in the brain structures. Biol Cybern. 1991;65:203-10. {% include badge doi="10.1007/BF00198091" pmid="1912013" %}
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. {% include badge doi="10.1016/j.neuroimage.2008.02.020" pmid="18394927" 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. {% include badge doi="10.1103/PhysRevLett.100.018701" pmid="18232831" %}
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. {% include badge doi="10.1016/j.neuroimage.2010.01.073" pmid="20114076" %}
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. {% include badge doi="10.1016/j.neuroimage.2011.01.055" pmid="21276857" %}
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. {% include badge doi="10.1007/s10827-011-0374-4" pmid="22187161" %}
Maris E. Statistical testing in electrophysiological studies. Psychophysiology. 2012;49(4):549-65. {% include badge doi="10.1111/j.1469-8986.2011.01320.x" pmid="22176204" %}
Maris E, Oostenveld R. Nonparametric statistical testing of EEG- and MEG-data. J Neurosci Methods. 2007;164(1):177-90. {% include badge doi="10.1016/j.jneumeth.2007.03.024" pmid="17517438" %}
Maris E, Schoffelen JM, Fries P. Nonparametric statistical testing of coherence differences. J Neurosci Methods. 2007 Jun 15;163(1):161-75. {% include badge doi="10.1016/j.jneumeth.2007.02.014" pmid="17391772" %}
Holm S. A simple sequentially rejective multiple test procedure. Scand J Stat. 1979;6(2):65-70. {% include badge jstor="4615733" %}
Hochberg Y. A sharper Bonferroni procedure for multiple tests of significance. Biometrika. 1988;75(4):800-2. {% include badge doi="10.1016/j.jneumeth.2007.02.014" %}
Genovese CR, Lazar NA, Nichols T. Thresholding of statistical maps in functional neuroimaging using the false discovery rate. Neuroimage. 2002;15(4):870-8. {% include badge doi="10.1006/nimg.2001.1037" pmid="11906227" %}
van Gerven MAJ, Hesse C, Jensen O, Heskes T. Interpreting single trial data using groupwise regularisation. Neuroimage. 2009;46(3):665-76. {% include badge doi="10.1016/j.neuroimage.2009.02.041" pmid="19285139" %}
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. {% include badge doi="10.1016/j.jneumeth.2009.01.016" pmid="19428515" %}
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. {% include badge doi="10.1038/s41596-018-0009-6" pmid="29988107" %}
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. {% include badge doi="10.1016/j.neuroimage.2022.119438" pmid="35792291" %}