title: TRENTOOL: a Matlab open source toolbox to analyse information flow in time series data with transfer entropy.
abstract: BACKGROUND
  Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present.
  
  
  RESULTS
  In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected.
  
  
  CONCLUSIONS
  TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox.
authors.affiliation: MEG Unit, Brain Imaging Center, Goethe University, Frankfurt, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Lindner
authors.forename: Raul
authors.initials: R
authors.lastname: Vicente
authors.forename: Viola
authors.initials: V
authors.lastname: Priesemann
authors.forename: Michael
authors.initials: M
authors.lastname: Wibral
mesh_terms: D000465:Algorithms; D000818:Animals; D015984:Causality; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D004569:Electroencephalography / Q000706:statistics & numerical data; D004596:Electroretinography; D019277:Entropy; D005189:False Positive Reactions; D006801:Humans; D007257:Information Theory; D016014:Linear Models; D008564:Membrane Potentials / Q000502:physiology; D016571:Neural Networks, Computer; D017711:Nonlinear Dynamics; D016011:Normal Distribution; D010775:Photic Stimulation; D015203:Reproducibility of Results; D012160:Retina / Q000502:physiology; D012984:Software; D013477:Superior Colliculi / Q000502:physiology; D014426:Turtles
references.citation: Comput Intell Neurosci. 2011;2011:852961
references.pmid: 21437221
references.citation: J Comput Neurosci. 2011 Feb;30(1):45-67
references.pmid: 20706781
references.citation: Phys Rev Lett. 2000 Jul 10;85(2):461-4
references.pmid: 10991308
references.citation: Biomed Tech (Berl). 2009 Dec;54(6):323-8
references.pmid: 19938889
references.citation: Neuroimage. 2003 Aug;19(4):1273-302
references.pmid: 12948688
references.citation: Spat Vis. 1997;10(4):437-42
references.pmid: 9176953
references.citation: J Neurosci Methods. 2007 Aug 15;164(1):177-90
references.pmid: 17517438
references.citation: J Neurosci Methods. 2010 Feb 15;186(2):262-73
references.pmid: 19961876
references.citation: J Neurosci. 2005 Apr 13;25(15):3962-72
references.pmid: 15829648
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Nov;66(5 Pt 1):051903
references.pmid: 12513519
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Jun;69(6 Pt 2):066138
references.pmid: 15244698
references.citation: Cell Tissue Res. 1983;234(1):219-24
references.pmid: 6640619
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2002 May;65(5 Pt 2):056201
references.pmid: 12059674
references.citation: Trends Cogn Sci. 2004 May;8(5):204-10
references.pmid: 15120678
references.citation: J Comput Neurosci. 2010 Dec;29(3):547-66
references.pmid: 20396940
references.citation: J Neurophysiol. 2007 Sep;98(3):1064-72
references.pmid: 17615128
references.citation: Comput Intell Neurosci. 2011;2011:156869
references.pmid: 21253357
references.citation: Phys Rev Lett. 2008 Jun 13;100(23):234101
references.pmid: 18643502
references.citation: PLoS One. 2009 Aug 04;4(8):e6482
references.pmid: 19652720
references.citation: J Comput Neurosci. 2011 Feb;30(1):7-16
references.pmid: 20333542
references.citation: Neuroimage. 2011 Sep 15;58(2):339-61
references.pmid: 21477655
references.citation: Brain Behav Evol. 1996;48(6):307-37
references.pmid: 8955961
references.citation: Neural Netw. 2008 Oct;21(8):1094-104
references.pmid: 18599267
references.citation: Biol Cybern. 2003 Feb;88(2):129-36
references.pmid: 12567227
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Feb;77(2 Pt 2):026110
references.pmid: 18352093
references.citation: Phys Rev Lett. 2009 Dec 4;103(23):238701
references.pmid: 20366183
references.citation: J Comput Neurosci. 2011 Feb;30(1):69-84
references.pmid: 20556639
references.citation: Int J Psychophysiol. 2008 Mar;67(3):200-11
references.pmid: 17692981
references.citation: PLoS Comput Biol. 2010 Sep 16;6(9):
references.pmid: 20862355
references.citation: Neuroimage. 2010 Jan 15;49(2):1593-600
references.pmid: 19698792
references.citation: J Neurosci Methods. 1999 Dec 15;94(1):105-19
references.pmid: 10638819
references.citation: Science. 1996 Sep 27;273(5283):1868-71
references.pmid: 8791593
references.citation: J Neurophysiol. 1990 May;63(5):1033-45
references.pmid: 2358861
references.citation: Front Hum Neurosci. 2008 Aug 20;2:7
references.pmid: 18958208
references.citation: Magn Reson Imaging. 2010 Oct;28(8):1113-9
references.pmid: 20409664
references.citation: Cogn Neurodyn. 2008 Jun;2(2):121-36
references.pmid: 19003479
references.citation: J Comput Neurosci. 2011 Feb;30(1):85-107
references.pmid: 20799057
references.citation: Spat Vis. 1997;10(4):433-6
references.pmid: 9176952
references.citation: Biomed Tech (Berl). 2006 Jul;51(2):64-9
references.pmid: 16915767
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Apr;63(4 Pt 2):046211
references.pmid: 11308934
references.citation: J Neurophysiol. 2007 Mar;97(3):2533-43
references.pmid: 17202243
references.citation: Neuroimage. 2010 Feb 15;49(4):3099-109
references.pmid: 19914382
references.citation: J Neurosci Methods. 2003 Apr 15;124(2):113-28
references.pmid: 12706841
references.citation: IEEE Trans Neural Syst Rehabil Eng. 2009 Jun;17(3):244-53
references.pmid: 19497831
references.citation: Prog Biophys Mol Biol. 2011 Mar;105(1-2):80-97
references.pmid: 21115029