<h1 align="center">
<a href="http://www.clinicadl.readthedocs.io">
<img src="https://clinicadl.readthedocs.io/en/latest/images/logo.png" alt="ClinicaDL Logo" width="120" height="120">
</a>
<br/>
ClinicaDL
</h1>
<p align="center"><strong>Framework for the reproducible processing of neuroimaging data with deep learning methods</strong></p>
<p align="center">
<a href="https://ci.inria.fr/clinicadl/job/AD-DL/job/dev/">
<img src="https://ci.inria.fr/clinicadl/buildStatus/icon?job=AD-DL%2Fdev" alt="Build Status">
</a>
<a href="https://badge.fury.io/py/clinicadl">
<img src="https://badge.fury.io/py/clinicadl.svg" alt="PyPI version">
</a>
<a href='https://clinicadl.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/clinicadl/badge/?version=latest' alt='Documentation Status' />
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<a href='https://pepy.tech/project/clinicadl'>
<img src='https://static.pepy.tech/badge/clinicadl/month' alt='Downloads' />
</a>
</p>
<p align="center">
<a href="https://clinicadl.readthedocs.io/">Documentation</a> |
<a href="https://aramislab.paris.inria.fr/clinicadl/tuto">Tutorial</a> |
<a href="https://groups.google.com/forum/#!forum/clinica-user">Forum</a>
</p>
## About the project
This repository hosts ClinicaDL, the deep learning extension of [Clinica](https://github.com/aramis-lab/clinica),
a python library to process neuroimaging data in [BIDS](https://bids.neuroimaging.io/index.html) format.
> **Disclaimer:** this software is **under development**. Some features can
change between different releases and/or commits.
To access the full documentation of the project, follow the link
[https://clinicadl.readthedocs.io/](https://clinicadl.readthedocs.io/).
If you find a problem when using it or if you want to provide us feedback,
please [open an issue](https://github.com/aramis-lab/ad-dl/issues) or write on
the [forum](https://groups.google.com/forum/#!forum/clinica-user).
## Getting started
ClinicaDL currently supports macOS and Linux.
We recommend to use `conda` or `virtualenv` for the installation of ClinicaDL
as it guarantees the correct management of libraries depending on common
packages:
```{.sourceCode .bash}
conda create --name ClinicaDL python=3.8
conda activate ClinicaDL
pip install clinicadl
```
## Tutorial
Visit our [hands-on tutorial web
site](https://aramislab.paris.inria.fr/clinicadl/tuto) to start
using **ClinicaDL** directly in a Google Colab instance!
## Related Repositories
- [Clinica: Software platform for clinical neuroimaging studies](https://github.com/aramis-lab/clinica)
- [AD-DL: Convolutional neural networks for classification of Alzheimer's disease: Overview and reproducible evaluation](https://github.com/aramis-lab/AD-DL)
- [AD-ML: Framework for the reproducible classification of Alzheimer's disease using machine learning](https://github.com/aramis-lab/AD-ML)
## Citing us
- Thibeau-Sutre, E., Díaz, M., Hassanaly, R., Routier, A., Dormont, D., Colliot, O., Burgos, N.: ‘ClinicaDL: an open-source deep learning software for reproducible neuroimaging processing‘, 2021. [hal-03351976](https://hal.inria.fr/hal-03351976)
- Routier, A., Burgos, N., Díaz, M., Bacci, M., Bottani, S., El-Rifai O., Fontanella, S., Gori, P., Guillon, J., Guyot, A., Hassanaly, R., Jacquemont, T., Lu, P., Marcoux, A., Moreau, T., Samper-González, J., Teichmann, M., Thibeau-Sutre, E., Vaillant G., Wen, J., Wild, A., Habert, M.-O., Durrleman, S., and Colliot, O.: ‘Clinica: An Open Source Software Platform for Reproducible Clinical Neuroscience Studies’, 2021. [doi:10.3389/fninf.2021.689675](https://doi.org/10.3389/fninf.2021.689675) [Open Access version](https://hal.inria.fr/hal-02308126)
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