https://github.com/aramis-lab/clinicadl

Framework for the reproducible processing of neuroimaging data with deep learning methods
https://github.com/aramis-lab/clinicadl

alzheimer-disease brain-imaging convolutional-neural-network deep-learning medical-imaging neuroimaging python pytorch

Last synced: 1 day ago
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Framework for the reproducible processing of neuroimaging data with deep learning methods

• Host: GitHub
• URL: https://github.com/aramis-lab/clinicadl
• Owner: aramis-lab
• License: mit
• Created: 2019-07-15T15:02:36.000Z (over 5 years ago)
• Default Branch: dev
• Last Pushed: 2024-05-22T14:05:16.000Z (6 months ago)
• Last Synced: 2024-05-22T14:33:43.510Z (6 months ago)
• Topics: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
• Language: Python
• Homepage: https://clinicadl.readthedocs.io/
• Size: 9.73 MB
• Stars: 152
• Watchers: 11
• Forks: 52
• Open Issues: 32
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE.txt
  • Citation: CITATION.cff

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  ClinicaDL



Framework for the reproducible processing of neuroimaging data with deep learning methods




  

    

  

  

    

  

  

    

  

  

    

  





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## 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=3.10

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)