clinicadl

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

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

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
✓
Committers with academic emails
4 of 17 committers (23.5%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (16.3%) to scientific vocabulary

Keywords

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

Keywords from Contributors

brainweb neuroscience ants bids-format freesurfer fsl mrtrix3 spm dataflow-engine workflow-engine

Last synced: 6 months ago · JSON representation ·

Repository

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

Basic Info

Host: GitHub
Owner: aramis-lab
License: mit
Language: Python
Default Branch: dev
Homepage: http://clinicadl.aramislab.fr/
Size: 128 MB

Statistics

Stars: 174
Watchers: 6
Forks: 60
Open Issues: 47
Releases: 25

Topics

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

Created over 6 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

ClinicaDL

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

Documentation | Tutorial | Forum

About the project

This repository hosts ClinicaDL, the deep learning extension of Clinica, a Python library to process neuroimaging data in BIDS 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/. If you find a problem when using it or if you want to provide us feedback, please open an issue or write on the forum.

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 to start using ClinicaDL directly in a Google Colab instance!

Related Repositories

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
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 Open Access version

Owner

Name: ARAMIS Lab
Login: aramis-lab
Kind: organization
Location: Paris, France

Website: www.aramislab.fr
Twitter: AramisLabParis
Repositories: 21
Profile: https://github.com/aramis-lab

The Aramis Lab is a joint research team between CNRS, Inria, Inserm and Sorbonne University and belongs to the Paris Brain Institute (ICM).

Citation (CITATION.cff)

cff-version: 1.6.1
message: If you use this software, please cite it as below.
authors:
  - family-names: Thibeau-Sutre
    given-names: Elina
  - family-names: Diaz
    given-names: Mauricio
  - family-names: Hassanaly
    given-names: Ravi
  - family-names: Routier
    given-names:  Alexandre
  - family-names: Dormont
    given-names: Didier
  - family-names: Colliot
    given-names: Olivier
  - family-names: Burgos
    given-names: Ninon
  - family-names: Vaillant
    given-names: Ghislain
  - family-names: Wen
    given-names: Junhao
  - family-names: Loizillon
    given-names: Sophie
  - family-names: Cassereau
    given-names: Nathan
  - family-names: Brianceau
    given-name: Camille
  - family-names: Gensollen
    given-names: Nicolas
title: "ClinicaDL: Framework for the reproducible processing of neuroimaging data with deep learning methods."
version: 1.4.0
doi: 10.1016/j.cmpb.2022.106818
license: MIT
date-released: 2023-06-09
url: "https://github.com/aramis-lab/clinicadl"

GitHub Events

Total

Create event: 14
Release event: 1
Issues event: 38
Watch event: 8
Delete event: 11
Issue comment event: 33
Push event: 54
Pull request review comment event: 78
Pull request review event: 92
Pull request event: 118
Fork event: 8

Last Year

Create event: 14
Release event: 1
Issues event: 38
Watch event: 8
Delete event: 11
Issue comment event: 33
Push event: 54
Pull request review comment event: 78
Pull request review event: 92
Pull request event: 118
Fork event: 8

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 1,598
Total Committers: 17
Avg Commits per committer: 94.0
Development Distribution Score (DDS): 0.524

Top Committers

Name	Email	Commits
Elina Thibeau--Sutre	e**e@i**g	760
Mauricio DIAZ	m**z@i**r	468
junhao.wen	a**6@h**m	164
Elina Thibeau-Sutre	e**s@f**r	49
Alexandre Routier	a**r@g**m	36
Ravi Hassanaly	4**8@u**m	24
camillebrianceau	5**u@u**m	24
WEN Junhao	j**n@l**g	16
ravih18	r**6@g**m	14
dependabot[bot]	4**]@u**m	11
nburgos	n**s@u**m	8
Ghislain Vaillant	g**l@u**m	8
Alexandre Routier	a**r@u**m	8
Ghislain Vaillant	g**t@i**g	5
Olivier Colliot	4**t@u**m	1
Camille Brianceau	c**u@g**m	1
NicolasGensollen	n**n@g**m	1

Committer Domains (Top 20 + Academic)

icm-institute.org: 2 login01.icm-institute.org: 1 free.fr: 1 inria.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 78
Total pull requests: 463
Average time to close issues: 8 months
Average time to close pull requests: 24 days
Total issue authors: 15
Total pull request authors: 16
Average comments per issue: 0.47
Average comments per pull request: 0.33
Merged pull requests: 325
Bot issues: 0
Bot pull requests: 62

Past Year

Issues: 27
Pull requests: 76
Average time to close issues: 15 days
Average time to close pull requests: 8 days
Issue authors: 5
Pull request authors: 4
Average comments per issue: 0.0
Average comments per pull request: 0.21
Merged pull requests: 43
Bot issues: 0
Bot pull requests: 8

View more stats

Top Authors

Issue Authors

thibaultdvx (21)
ravih18 (14)
camillebrianceau (9)
mselimata (6)
NicolasGensollen (6)
chgodard (5)
14thibea (5)
mtmmu88 (4)
souravraha (2)
msolal (1)
acasamitjana (1)
HuguesRoy (1)
J-V1 (1)
MatthieuJoulot (1)
naji-s (1)

Pull Request Authors

camillebrianceau (239)
thibaultdvx (76)
dependabot[bot] (62)
NicolasGensollen (35)
ravih18 (12)
sophieloiz (7)
ghisvail (7)
ncassereau-idris (5)
HuguesRoy (4)
14thibea (4)
mdiazmel (4)
msolal (2)
sofiene26000 (2)
nburgos (2)
mselimata (1)

Top Labels

Issue Labels

enhancement (12) refactoring (11) good first issue (9) documentation (9) bug (8) solved (1) dependencies (1) tests (1)

Pull Request Labels

refactoring (90) dependencies (62) python (54) enhancement (7) bug (6) duplicate (2) documentation (1)

Packages

Total packages: 1
Total downloads:
- pypi 101 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 34
Total maintainers: 4

pypi.org: clinicadl

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

Homepage: https://clinicadl.readthedocs.io
Documentation: https://clinicadl.readthedocs.io
License: MIT
Latest release: 1.6.1
published almost 2 years ago

Versions: 34
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 101 Last month

Rankings

Forks count: 5.9%

Stargazers count: 5.9%

Dependent packages count: 10.1%

Average: 12.4%

Downloads: 18.7%

Dependent repos count: 21.5%

Maintainers (4)

aramis ghisvail NicolasGensollen mdiaz

Last synced: 6 months ago

Dependencies

poetry.lock pypi

116 dependencies

pyproject.toml pypi

black * develop
isort * develop
pre-commit * develop
pytest * develop
pytest-cov ^3.0.0 develop
pytest-timeout * develop
pytest-xdist * develop
click ^8
click-option-group ^0.5
clinica ^0.5.5
mkdocs ^1.1
mkdocs-material *
numpy ^1.17
pandas ^1.2
pymdown-extensions *
pynvml *
python ^3.7.1
scikit-image ^0.19
scikit-learn ^1.0
tensorboard *
toml *
torch ^1.8.0
torchvision *

.github/workflows/lint.yaml actions

actions/checkout v4 composite
actions/setup-python v4 composite

.github/workflows/publish.yaml actions

actions/checkout v4 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish release/v1 composite

.github/workflows/test.yml actions

actions/checkout v4 composite
actions/setup-python v4 composite
snok/install-poetry v1 composite

environment.yml conda

python 3.9.*

clinicadl

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

ClinicaDL

About the project

Getting started

Tutorial

Related Repositories

Citing us

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: clinicadl

Rankings

Maintainers (4)

Dependencies