# References to implemented methods

This list is far from complete, many more algorithms that have been published in papers are implemented in FieldTrip. 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 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. If allowed, you can also upload a pdf version to the website and provide a link here.

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

## 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

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.

### 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 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.

### Forward model solution for EEG, using FEM

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).

## 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, Hamalainen 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: 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.

### Distributed source reconstruction using linear estimation

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. Hamalainen, 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.

### 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 Morletâ€™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.

## 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 J-M, Oostenveld R. Online and offline tools for head movement compensation in MEG. NeuroImage. 2013.

## Scalp current density mapping

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.

## Planar gradient computation

Bastiaansen, M. C. M., & Knsche, T. R. (2000). MEG tangential derivative mapping applied to Event-Related Desynchronization (ERD) research. Clinical Neurophysiology, 111, 1300-1305.

## Connectivity analysis

### General tutorial + some things to think about

Bastos and Schoffelen A Tutorial Review of Functional Connectivity Analysis Methods and Their Interpretational Pitfalls Front. Syst. Neurosci., 08 January 2016.

### Coherence

Rosenberg et al. The Fourier approach to the identification of functional coupling between neuronal spike trains. Prog Biophys Molec Biol 1989; 53; 1-31

### Phase locking value

Lachaux et al. Measuring phase sychrony in brain signals. Human Brain Mapping, 1999; 8; 194-208

### Partial coherence

Rosenberg et al. 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 et al. Identifying true brain interaction from EEG data using the imaginary part of coherence. Clinical Neurophysiology, 2004; 115; 2292-2307

### Phase slope index

Nolte et al. Robustly estimating the flow direction of information in complex physical systems. Physical Review Letters, 2008; 100; 234101

### Partial directed coherence

Baccala and Sameshima. Partial directed coherence: a new concept in neural structure determination. Biol. Cybern., 2001; 84; 463-474

### Directed transfer function

Kaminski and Blinowska. A new method of the description of the information flow in the brain structures. Biol. Cybern., 1991; 65; 203-210

### Spectrally resolved Granger causality

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.

### Pairwise Phase Consistency

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

### Weighted Phase Lag Index

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

### Spike-LFP phase-coupling measures

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

## Statistics for EEG- and MEG-data

Maris E. Statistical Testing in Electrophysiological Studies Psychophysiology (2012) Vol 49 No 4, pp. 549-65.

### Statistical inference by means of permutation

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.

### Multiple comparison corrections

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.

### Machine learning

Van Gerven, M.A.J., Hesse, C., Jensen, O., Heskes, T. Interpreting Single Trial Data using Groupwise Regularisation. Neuroimage. 2009; 46(3):665-76.

## Brain-computer interfacing

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.

## Intracranial EEG analysis

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