- the Transfer Entropy Toolbox for the Fieldtrip data format.
Coypright (C) 2009, Michael Lindner, Raul Vicente and Michael Wibral
Coypright (C) 2012, Michael Lindner, Raul Vicente, Michael Wibral, Nicu Pampu and Patricia Wollstadt, Viola Priesemann
Coypright (C) 2012, Michael Lindner, Raul Vicente, Michael Wibral, Nicu Pampu and Patricia Wollstadt, Viola Priesemann, Mario Martinez-Zarzuela
TRENTOOL acknowledges the support of :
Research Grant LOEWE-NeFF 'Neuronale Koordination Forschungsschwerpunkt Frankfurt' (MW,RV,NP, MMZ)
TRENTOOL is distributed under the GNU public license version 3 (or later)
We moved the TRENTOOL source code to the GitHub repository. Please use the services provided there to view the code, collaborate etc. We will from now on also use the GitHub issue tracker and wiki.
Related Sites and Software
- A small simulation and plotting tool was kindly provided by Felix Siebenhuehner and can be downloaded here. (NOTE: by downloading you accept the terms of the GPL v3 license). As usual the code comes as is and without any warranty.
- We appreciate any kind of feedback: suggestions for features, usability improvements, crash reports etc.,!
- We are really happy there is a lively community around tranfer
entropy and information theory in complex systems. If our toolbox
doesn'tmake you happy, be sure to also check out what our friends have
done: (1) the magnificent all in one Java information dynamics toolkit
by Joe Lizier that provides localized measures of information transfer
and storage and general purpose mutual information estimators, (2) the MuTE
toolbox for multivariate information transfer by Alessandro Montalto,
based on work by Luca Faes and Daniele Marinazzo. If you know more
toolboes from this domain, let us know.
Status and News
2015-0206 Attention MAC users:
At the TRENTOOL workshop at UCL we noticed that TRENTOOL doesn't work
for mac because of missing mex files for the maci64 archtitecture. This has been resolved, the current version of the toolbox provides mex files for both 32 and 64bit Mac architectures.
Thanks to Patricia Wollstadt, the new Version 3.3 is available
for download now, including a new manual. Version 3.3 contains a
rewrite of some statistics functions and brings a many fold speedup
when searching for the correct delays of the information transfer (~
number of delays searched for). Additional thanks go to Joe Lizier for
pointing out further code changes for speeding up TRENTOO.
2014-07-24 TRENTOOL's GPU routines are being ported to OPENCL, to make users with non-nvidia hardware happy, too.
2014-06-13 Bugfix in the routines computing the embedding delay ('tau'). Please update to the latest verison 3.2.
2013-06-21 Thanks to the very hard work of Mario Martinez Zarzuela and
Patricia Wollstadt a stable TRENTOOL version for the analysis of
nonstatinary data via the ensemble method of Gomez-Herrero and Vicente (http://arxiv.org/abs/1008.0539)
is available. Note that you will need a larger amount of trials than
usual to make this work nicely (at least 150 trials of 100ms at 1.2kHz
sampling rate is recommended). Due to the necessary changes in
surrogate statistics for the ensemble method, this will only run
with GPU acceleration. The code for the next neighbour search on GPU
was written by Mario in CUDA. When 'installing' TRENTOOL you will now
have to run a little compiler script in MATLAB to compile the CUDA code
for your card (if you want to use this functionality). To use it, you
will need a CUDA capable graphics card. There is no need to heavily
invest though as a gtx 580 should work (the algorithm uses single
precision arithmetics for now, as this is what our EEGs and MEGs
deliver in useful resolution anyway).
Downlaod the latest version (3.0) here.
2013-04-02 Analysis of non-stationary time series is now possible: New routines for the ensemble approach suggest by Gomez-Herrero and Raul Vicente (here),
have been implemented together with the corresponding statistical tools
by Mario Martinez Zarzuela and Patricia Wollstadt. You will need a
CUDA-capable GPU (e.g. gtx580 is fine) to run this code. Contact us via
email for a beta version of the code.
Support for the MATLAB paralle computing toolbox added - see the header
of TEsurrogatestats.m for help on the new options in the configuration
Presentation at EBMC 2012 San Diego on the model-free reconstruction of
interaction delays with transfer entropy. A paper in the conference
proceedings should appear soon. Another paper detailing the
mathematical theory behind delay reconstruction with transfer entropy
Thanks to the work of Nicu Pampu and Patricia Wollstadt, version 2.0.3
adds the possibility to reconstruct the delays of interactions and to
use these reconstructed interaction delays to mark potentially spurious
interactions in the graph (cascade effects, common drive effects).
Moreover second-level binomial statistics have been added to check for
the existence of a direcetd interaction (at the group level).
Updated the example script below with a comment demonstrating how to
use cfg.sgncmb to analyze only specific signal combinations (which
might save a lot of time, if one is only interested in these).
2012-04-30 The TRENTOOL course seems to have been a great success. Please find the course slides here. The new version (2.0.0) is available for download (see above). There are also the Course materials.
Note that these examples run if you set the paths in the scripts
accordingly, and they run only on Matlab 2008b or higher and only on
Linux 64 bit machines (Win and Mac users will have get other variants
of the TSTool toolbox (see Installation below)).
2012-02-17 Two new developers joined the TRENTOOL team. We
officially welcome Nicu Pampu from the Coneural Institute in
Kluj-Napoca, Rumania and Patricia Wollstadt from Goethe University
Frankfurt as new developers. Nicu has ported TRENTOOL to MATLAB's
parallel computing toolbox, and will look into CUDA support. Patricia
is working on graph-theoretical extesion to the toolbox. These changes
will be available upon release of TRENTOOL2. Beta-testers may contact
michael.wibral <AT> web.de.
2012-02-17 TRENTOOL course announcement.
Togther with the NeFF Symposium on "Non-linear and model-free measures
of directed interactions in neuroscience" there will be a two-afternoon
course for TRENTOOL users. Reistration fee for course and symposium
will be 50 EUR. To apply send an email to michael.wibral <at>
2012-02-17 A new experimental version of TRENTOOL2
is available which offers better organisation of the code and
additional features, including experiemntal support for MATLABs
parallel computing toolbox. Please send an email to michael.wibral
<at> web.de if you are interested in beta-testing.