:orphan:

The pyNIBS documentation.
=========================
**pyNIBS** is a Pyhon package to work with non-invasive brain stimulation (NIBS) data, foremost from transcranial magnetic stimulation (TMS) experiments.

We created this package to allow the mapping of causal structure-function relationships with TMS. A lot of analyses is based on calculations of the induced electric fields (e-fields) -- for this we rely on `SimNIBS <https://simnibs.github.io/simnibs/>`_.

Install **pyNIBS** via `pip <https://pypi.org/project/pynibs/>`_:

.. code-block:: bash

    pip install pynibs

or directly grab from our repository at `gitlab.gwdg.de/tms-localization/pynibs <https://gitlab.gwdg.de/tms-localization/pynibs>`_



Contents.
=========
.. toctree::
   :maxdepth: 1

   pynibs
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


References.
===========
- Numssen*, O., Martin*, C. W., Worbs, T., Thielscher, A., Weise, K., & Knösche, T. R. (2025). Optimizing and assessing multichannel TMS focality. *bioRxiv*. doi: `10.1101/2025.09.19.677136 <https://doi.org/10.1101/2025.09.19.677136>`_
- Jing, Y., Numssen, O., Hartwigsen, G., Knösche, T. R., & Weise, K. (2024). Effects of Electric Field Direction on TMS-based Motor Cortex Mapping. *bioRxiv*. doi: `10.1101/2024.12.10.627753 <https://doi.org/10.1101/2024.12.10.627753>`_
- Weise, K., Makaroff, S. N., Numssen, O., Bikson, M., & Knösche, T. R. (2025). Statistical method accounts for microscopic electric field distortions around neurons when simulating activation thresholds. *Brain Stimulation, 18*(2), 280–286. doi: `10.1016/j.brs.2025.02.007 <https://doi.org/10.1016/j.brs.2025.02.007>`_
- Numssen, O., Martin, S., Williams, K., Knösche, T. R., & Hartwigsen, G. (2024). Quantification of subject motion during TMS via pulsewise coil displacement. *Brain Stimulation, 17*(5), 1045–1047. doi: `10.1016/j.brs.2024.08.009 <https://doi.org/10.1016/j.brs.2024.08.009>`_
- Numssen*, O., Kuhnke*, P., Weise, K., & Hartwigsen, G. (2024). Electric field based dosing for TMS. *Imaging Neuroscience*. doi: `10.1162/imag_a_00106 <https://doi.org/10.1162/imag_a_00106>`_
- Jing, Y., Numssen, O., Weise, K., Kalloch, B., Buchberger, L., Haueisen, J., Hartwigsen, G., Knösche, T. (2023). Modeling the Effects of Transcranial Magnetic Stimulation on Spatial Attention. *Physics in Medicine & Biology*. doi: `10.1088/1361-6560/acff34 <https://doi.org/10.1088/1361-6560/acff34>`_
- Weise*, K., Numssen*, O., Kalloch, B., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R. (2022). Precise transcranial magnetic stimulation motor-mapping. *Nature Protocols*. doi: `10.1038/s41596-022-00776-6 <https://doi.org/10.1038/s41596-022-00776-6>`_
- Numssen*, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. *NeuroImage, 245*, 118654. doi:`10.1016/j.neuroimage.2021.118654 <https://doi.org/10.1016/j.neuroimage.2021.118654>`_
- Weise*, K., Numssen*, O., Thielscher, A., Hartwigsen, G., & Knösche, T. R. (2020). A novel approach to localize cortical TMS effects. *Neuroimage, 209*, 116486. doi: `10.1016/j.neuroimage.2019.116486 <https://doi.org/10.1016/j.neuroimage.2019.116486>`_