HERramientas de MEdida de la Sincronización
Tools for the Assessment of Synchronization

Please cite:

Niso, G., Bruña, R., Pereda, E., Gutiérrez, R., Bajo, R., Maestú, F., & del-Pozo, F. (2013). HERMES: towards an integrated toolbox to characterize functional and effective brain connectivity. Neuroinformatics, 11(4), 405-434. DOI: 10.1007/s12021-013-9186-1.

The toolbox

The latest version of the toolbox is available for download here.

Besides, we offer also for download some example data to start testing the toolbox

  • MEG example data: is available for download here
  • Synthetic example data: from two coupled dynamical nonlinear systems is available for download here

HERMES, as other signal processing software such as FieldTrip and SPM8, is distributed as a Matlab® toolbox. The source code is distributed along with some precompiled and obfuscated routines, to improve its performance. HERMES is distributed as open source, and is protected by the GPL license. This means that you can use it without limitation, change any part you want and re-distribute it, but always acknowledging the original authorship of the software.

The user guide

The estimation of synchronization indexes is in some way complex and very dependent of interpretation. In many cases, the indexes proposed in this toolbox require the specification of one or more parameters, and the output is highly dependent on them. In the manual of the toolbox, each index is detailed along with its parameters and the input and output range of values accepted.

  • Preprint version of the paper: is available for download here.
  • Quick start guide: is available for download here.
  • Video tutorial: is available here.

The algorithms, options and parameters may vary along different versions of HERMES. Make sure you are using the right version of the manual, corresponding with the version of the toolbox you plan to use.


To ensure the correct working of the toolbox, Matlab® R2012a (version 7.14) is required, along with Signal processing toolbox and Statistics toolbox. However it is possible (although we DO NOT guarantee it) that the toolbox also works with earlier versions of Matlab® (mainly 7.x , where x<14).