Metadata-Version: 2.1
Name: pynibs
Version: 0.2022.8
Summary: A python toolbox to conduct non-invasive brain stimulation experiments (NIBS).
Home-page: UNKNOWN
Author: Konstantin Weise, Ole Numssen
Author-email: kweise@cbs.mpg.de
License: GPL3
Project-URL: Home, https://gitlab.gwdg.de/tms-localization/pynibs
Project-URL: Docs, https://pynibs.readthedocs.io/
Project-URL: Twitter, https://www.twitter.com/num_ole
Project-URL: Download, https://pypi.org/project/pynibs/
Keywords: NIBS,non-invasive brain stimulation,TMS,FEM
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development :: Build Tools
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# pyNIBS
Preprocessing, postprocessing, and analyses routines for non-invasive brain stimulation experiments.

[![Latest Release](https://gitlab.gwdg.de/tms-localization/pynibs/-/badges/release.svg)](https://gitlab.gwdg.de/tms-localization/pynibs)
[![Documentation](https://readthedocs.org/projects/pynibs/badge/)](https://pynibs.readthedocs.io/)
[![pipeline status](https://gitlab.gwdg.de/tms-localization/pynibs/badges/-/pipeline.svg?ignore_skipped=true)](https://gitlab.gwdg.de/tms-localization/pynibs/commits/master)
[![coverage report](https://gitlab.gwdg.de/tms-localization/pynibs/badges/-/coverage.svg)](https://gitlab.gwdg.de/tms-localization/pynibs/commits/master)

![](https://gitlab.gwdg.de/uploads/-/system/project/avatar/9753/Fig_4.png?width=128)

`pyNIBS` provides the functions to allow **cortical mappings** with transcranial magnetic stimulation (TMS) via **functional analysis**. `pyNIBS` is developed to work with [SimNIBS](http://www.simnibs.org), i.e. SimNIBS' meshes and FEM results can directly be used.
 Currently, [SimNIBS 3.2.5](https://github.com/simnibs/simnibs/releases/download/v3.2.5/simnibs-3.2.5-cp37-cp37m-linux_x86_64.whl) is supported. Have a look at our [gitlab repository](https://gitlab.gwdg.de/tms-localization/pynibs) for SimNIBS 4 (beta) support.

See the [documentation](https://pynibs.readthedocs.io/en/latest/) for package details and our [protocol](https://protocolexchange.researchsquare.com/article/pex-1780/v1) publication for an extensive example of the usage.

## Installation
Via pip:

``` bash
pip install pynibs
```

Or clone the source repository and install via `setup.py`:

``` bash
git clone https://gitlab.gwdg.de/tms-localization/pynibs
cd pynibs
python setup.py develop
```

To import CED Signal EMG data use the `export to .mat` feature of Signal. 
To read .cfs files exported with CED Signal you might need to [manually](HOW_TO_INSTALL_BIOSIG.txt) compile the libbiosig package.


## Bugs
For sure. Please open an [issue](https://gitlab.gwdg.de/tms-localization/pynibs/-/issues) or feel free to file a PR.


## Citation
Please cite _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)_ when using this toolbox in your research.


## References
  - 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)
  - 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., Kalloch, B., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R. (2022). Precise transcranial magnetic stimulation motor-mapping. Nature Protocols. (accepted) 


