This is a preliminary version of our code. More features will be added soon! cdn-fmri is a Python-based package implementing causal dynamic network analysis for Functional magnetic resonance imaging (fMRI). It aims to improve the dynamic causal modeling with the optimization based method. Our optimization-based method and algorithm compute efficiently the ODE parameters from fMRI data, instead of comparing potentially a huge number of candidate ODE models. For a detailed introduction of dynamic causal modeling, see (1). For a sparse version of this package, see (2). This version may perform better in some cases.
@article{cao2019functional, title={A Functional Data Method for Causal Dynamic Network Modeling of Task-related fMRI}, author={Cao, Xuefei and Sandstede, Bjorn and Luo, Xi}, journal={Frontiers in Neuroscience}, volume={13}, pages={127}, year={2019}, publisher={Frontiers} }
This package supports both python 2.7 and python 3.6.
The example provided in the repo has been tested in mac os and Linux environment.
These instructions will get you a copy of the project up running on your local machine for development and testing purposes.
This package is also published in pypi. For a quick installation, try
pip install cdn-fmri
What things you need to install the software and how to install them
See setup.py for details of packages requirements.
Download the packages by using git clone https://github.com/xuefeicao/cdn.git
python setup.py install
If you experience problems related to installing the dependency Matplotlib on OSX, please see https://matplotlib.org/faq/osx_framework.html
After installing our package locally, try to import cdn in your python environment and learn about package's function. Note: our package name in pypi is cdn-fmri.
import cdn.cdn_analysis as cdn_analysis
help(cdn_analysis.cdn_multi_sub)
The examples subfolder includes a basic analysis of CDN analysis.
- Python 2.7
- python 2.7
- python 3.6
- Xuefei Cao - Maintainer - (https://github.com/xuefeicao)
- Björn Sandstede (http://www.dam.brown.edu/people/sandsted/)
- Xi Luo (http://bigcomplexdata.com/)
This project is licensed under the MIT License - see the LICENSE file for details