SimNIBS 2.1.1 Documentation

This documentation is thought to give a brief overview over SimNIBS 2.1 in a step-by-step fashion. It is based on the new example data set (containing a new realistic head model, an extended MNI head covering the neck and a sphere model). So please first download and unpack it.

• This tutorial describes all steps from setting up simulations in the graphical user interface (GUI) to visualizing the results in Gmsh and freeview.

• In addition, the features of the GUI are described in this documentation.

• SimNIBS 2.1 offers two programs (mri2mesh or alternatively the new headreco) to automatically create high-quality head meshes from MRI data. They are described in the documentation of the command-line tools. The latter also lists the new tools to create EEG positions and transform data between subject and MNI space.

• This preprint covers the basics of SimNIBS and goes into depth about group analysis. The group analysis data set can be found here

• Example matlab scripts to prepare simulations and to extract some key parameters from the simulation results can be found in the subdirectory matlab/examplesof the SimNIBS installation.

• We also provide example python scripts, located in the python_examples folder. Please run python scripts using the simnibs_python interpreter

• SimNIBS uses either FreeSurfer and FSL BET (mri2mesh) or SPM12 and CAT12 (headreco) to segment the head. The accuracy of these segmentations strongly depends on the MR sequences used to image the head. Some information on the sequences which we use can be found here.

• For the changelog, please follow this link
• For documentation on the old 2.0.1 version, please follow this link