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Welcome

This is the Wiki System of the SimBio software package.

SimBio is an open source toolbox for Electroencephalography (EEG) and Magnetoencephalography (MEG) source analysis as well as for the simulation of transcranial electric stimulation (tES). It can thus also be used for optimization of targeted brain stimulation using multi-electrode setups. Check the references to see some of the work that has been published with SimBio.

We started with the SimBio code development within the EU Framework V Project No. IST-1999-10378, from 2000 to 2003, see old SimBio webpage. The SimBio software consists of two subpackages:

  • IPM (Inverse Problem Method) toolbox containing algorithms for inverse EEG and MEG source analysis. IPM additionally contains analytical and quasi-analytical formulas for the EEG and MEG forward problem in multilayer spherical volume conductor models as well as Boundary Element Method (BEM) solutions for the EEG and MEG forward problem in realistically-shaped multi-compartment isotropic volume conductors and is written in C++.
  • NeuroFEM, which allows Finite Element Method (FEM) based EEG and MEG as well as tES forward solutions. NeuroFEM was based on the CAUCHY developments. The outer shell of the NeuroFEM code is written in C++ and allowed the embedding into IPM. The kernel FEM computation routines were adopted from CAUCHY and are therefore still in Fortran77.

Since 2013, the full SimBio code (IPM and NeuroFEM) is open-source code, please study the license agreement. You should know that SimBio is a "University-code", we unfortunately don't have any software-manager. We normally cannot give support, the only possibility for support is a cooperation or common research-project or similar. Here are two possibilities how to use our code developments:

  • The full SimBio C++/Fortran source code should be used together with the test-datasets, which offer a good start in using SimBio. For further reading, we refer to https://www.mrt.uni-jena.de/simbio/index.php/How_to. If you want to contribute to the sources, then you need to become a member of the SimBio developers group at sourceforge.net. In this case, please contact Hermann Sonntag via mail hsonntag'at'cbs.mpg.de.
  • If you just want to use an easily accessible SimBio-MATLAB code: Please see the Fieldtrip-SimBio documentation that can be cited by the following conference abstract, i.e., a poster that has been presented on the BACI conference in Geneva in Sept.2013. You also find this abstract here as Fieldtrip-SimBio-MATLAB. The FEM computation of EEG leadfields is probably the most interesting part of our code developments. To make this easier accessible than through the full SimBio code, we have been and will be working towards an integration of the NeuroFEM-pipeline into Fieldtrip and other toolboxes so that FEM-computed EEG leadfields can be used in other software pipelines. We would also like to integrate the NeuroFEM-MEG part and tES and TMS into other tools, but will first need to find a sponsor for it.

How to get a login?

This SimBio MediaWiki should now be freely accessible. If you have problems with it just get in touch with the site administrator Daniel.

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