kiragy/dynfc

dynFC: CoDe-Neuro's Dynamic Functional Connectivity Tools

This repository contains a Python module consisting of a set of tools developed to infer connectivity from fMRI (BOLD) signals. The module contains both phase-lock and correlation (+ cofluctuation) methods. Please be aware that this is still a develepment version and so may contain bugs and limited functionalities.

If you have any questions or suggestions, please open an issue in the relevant tab.

Please do not hesitate to suggest improvements to this module.

Citation

⚠️ Please, use the following article for reference:

Lucas G. S. França, Judit Ciarrusta, Oliver Gale-Grant, Sunniva Fenn-Moltu, Sean Fitzgibbon, Andrew Chew, Shona Falconer, Ralica Dimitrova, Lucilio Cordero-Grande, Anthony N Price, Emer Hughes, Jonathan O’Muircheartaigh, Eugene Duff, Jetro J Tuulari, Gustavo Deco, Serena J Counsell, Joseph V Hajnal, Chiara Nosarti, Tomoki Arichi, A David Edwards, Grainne McAlonan, Dafnis Batalle. bioRxiv 2022.11.16.516610; doi: https://doi.org/10.1101/2022.11.16.516610

Installation

The easiest way to install dynfc is via pip (PyPI) with the command below.

pip install dynfc

If you would like to specify a version use the following command to install version 0.0.1a1, for example.

pip install dynfc==0.0.1a1

Alternatively one can clone this repository and add it to a project. For that use the following command.

git clone https://github.com/CoDe-Neuro/

Built on

Numpy	Scipy

The data used for testing was obtained from the repository brain-networks/edge-ts. [no license]

Please find references for the methods available here in the relevant docs for each function.

Funding

This project is funded by a Wellcome Trust Seed Award in Science [217316/Z/19/Z].

License

MIT License

Copyright (c) 2021 Lucas G. S. França and Dafnis Batallé

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.