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Functional alignment of fMRI data in Python

Project description

# fmralign [Functional alignment and template estimation library](https://parietal-inria.github.io/fmralign-docs) for functional Magnetic Resonance Imaging (fMRI) data

This library is meant to be a light-weight Python library that handles functional alignment tasks. It is compatible with and inspired from [Nilearn](http://nilearn.github.io).

Alternative implementations of these ideas can be found in the [pymvpa](http://www.pymvpa.org) or [brainiak](http://brainiak.org) packages.

## Getting Started

### Prerequisites

fmralign requires a Python installation and the following dependencies: * Python >= 3.6 * Numpy >= 1.16.2 * SciPy >= 1.2.2 * Scikit-learn >= 0.20 * Matplotlib >= 3.1.1 * Nibabel >= 2.5.0 * Nilearn >= 1.5.0

### Installation

Open a terminal window, go the location where you want to install it. Then run:

` pip install fmralign `

Or if you want the latest version available (for example to develop):

` git clone https://github.com/Parietal-INRIA/fmralign.git cd fmralign pip install -e . `

Optionally, if you want to use optimal transport based method, you should also run:

` pip install POT `

You’re up and running!

### Documentation

You can found an introduction to functional alignment, a user guide and some examples on how to use the package at https://parietal-inria.github.io/fmralign-docs.

## License

This project is licensed under the Simplified BSD License.

## Acknowledgments

This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 785907 (HBP SGA2). This project was supported by [Digiteo](http://www.digiteo.fr).

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