.. simnibs documentation master file, created by
   sphinx-quickstart on Wed Aug 22 14:44:31 2018.

==========
 SimNIBS 4
==========


**SimNIBS 4** is a free and open source software package for the Simulation of Non-invasive Brain Stimulation. It allows for realistic calculations of the electric field induced by transcranial magnetic stimulation (TMS) and transcranial electric stimulation (TES). 

A SimNIBS workflow consists of three main parts:

   * :ref:`Generate high-quality head models <head_modeling_tutorial>` from MR images.

   * Set up and run simulation using our fast FEM solvers in the :ref:`graphical user interface <gui_tutorial>`, or via :ref:`MATLAB or Python scripts <scripting_tutorial>`.

   * :ref:`Visualize simulation results <visualization_tutorial>`, and easily transform them to *FsAverage* or *MNI* space via in-built functions.

SimNIBS offers several advanced options such as :ref:`Optimizations of TMS coil positions <tms_optimize>`, or TES optimizations for :ref:`single and multiple targets <tdcs_opt>` and :ref:`brain network targeting <tdcs_distributed_opt>`.

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  SimNIBS is being developed at the <a href="https://www.drcmr.dk">Danish Research Centre for Magnetic Resonance (DRCMR)</a> and the <a href="https://www.dtu.dk/english">Technical University of Denmark (DTU)</a>, in collaboration with <a href="contributors.html" >external partners</a>
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SimNIBS is copyrighted |copy| by its :ref:`authors <contributors>` and licensed under :download:`GPL v3 <../LICENSE.txt>`.


.. note:: When you publish results based on SimNIBS, please cite `Thielscher, A., Antunes, A. and Saturnino, G.B. (2015), Field modeling for transcranial magnetic stimulation: a useful tool to understand the physiological effects of TMS? IEEE EMBS 2015, Milano, Italy <http://dx.doi.org/10.1109/EMBC.2015.7318340>`_

  Please see :ref:`our publications <publications>` for details about the SimNIBS modules.

.. warning:: SimNIBS is a research tool. Clinical usage is not supported or advised. In particular, SimNIBS was not tested to give accurate results in the presence of pathological condition

.. |copy| unicode:: U+000A9

======
 News
======

  * **Version 4.1.0** improves the mesh quality and adds the option to use FreeSurfer results for more accurate representation of smaller sulci in the head meshes
  * Version 4.0.0 is a major update that introduces our new head modeling approach :ref:`charm <head_modeling_tutorial>`. In contrast to the previous methods, *charm* does not have any external dependencies (matlab, freesurfer) and is ready-to-run directly after installation. Head models created by *charm* are more accurate for non-brain tissues and include additional tissue types such as large blood vessels and spongy bone.
  * *Charm* replaces the previous methods *mri2mesh* and *headreco* which are discontinued. Use the tool :ref:`convert_3_to_4` to convert old head models for use in SimNIBS4 simulations.
  * Further major new features are the inclusion of :ref:`many new TMS coil models <coil_fies>` and a :ref:`flexible meshing approach <fixheadmodel_tutorial>` to simplify manual editing and inclusion of custom tissue types in the head mesh. Basic I/O functions for :ref:`neuronavigation data <nnav_docs>` are now also available in python. 

Please see details in the :ref:`changelog <changelog>`.

.. toctree::
   :maxdepth: 2
   :hidden:

   installation/installation
   dataset
   tutorial/tutorial
   documentation/documentation
   faq
   gallery
   contributors
   publications
   changelog
   contact