clinica

Software platform for clinical neuroimaging studies

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
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 5 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
21 of 55 committers (38.2%) from academic institutions
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Institutional organization owner
○
JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary

Keywords

ants bids-format brainweb freesurfer fsl machine-learning mrtrix3 neuroimaging neuroscience python scikit-learn spm

Keywords from Contributors

brain-imaging standardization dataflow dataflow-programming workflow-engine mvpa fmri decoding brain-mri brain-connectivity

Last synced: 6 months ago · JSON representation ·

Repository

Software platform for clinical neuroimaging studies

Basic Info

Host: GitHub
Owner: aramis-lab
License: other
Language: Python
Default Branch: dev
Homepage: http://www.clinica.run/
Size: 35.4 MB

Statistics

Stars: 257
Watchers: 15
Forks: 88
Open Issues: 83
Releases: 47

Topics

ants bids-format brainweb freesurfer fsl machine-learning mrtrix3 neuroimaging neuroscience python scikit-learn spm

Created almost 7 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Citation

Clinica

Software platform for clinical neuroimaging studies

Homepage | Documentation | Paper | Forum | See also: AD-ML, AD-DL, ClinicaDL

About The Project

Clinica is a software platform for clinical research studies involving patients with neurological and psychiatric diseases and the acquisition of multimodal data (neuroimaging, clinical and cognitive evaluations, genetics...), most often with longitudinal follow-up.

Clinica is command-line driven and written in Python. It uses the Nipype system for pipelining and combines widely-used software packages for neuroimaging data analysis (ANTs, FreeSurfer, FSL, MRtrix, PETPVC, SPM), machine learning (Scikit-learn) and the BIDS standard for data organization.

Clinica provides tools to convert publicly available neuroimaging datasets into BIDS, namely:

Clinica can process any BIDS-compliant dataset with a set of complex processing pipelines involving different software packages for the analysis of neuroimaging data (T1-weighted MRI, diffusion MRI and PET data). It also provides integration between feature extraction and statistics, machine learning or deep learning.

ClinicaPipelines

Clinica is also showcased as a framework for the reproducible classification of Alzheimer's disease using machine learning and deep learning.

Getting Started

Full instructions for installation and additional information can be found in the user documentation.

Using pipx (recommended)

Clinica can be easily installed and updated using pipx.

console pipx install clinica

Using pip

console pip install clinica

Using Conda

Clinica relies on multiple third-party tools to perform processing.

An environment file is provided in this repository to facilitate their installation in a Conda environment:

console git clone https://github.com/aramis-lab/clinica && cd clinica conda env create conda activate clinica

After activation, use pip to install Clinica.

Additional dependencies (required)

Depending on the pipeline that you want to use, you need to install pipeline-specific interfaces. Some of which uses a different runtime or use incompatible licensing terms, which prevent their distribution alongside Clinica. Not all the dependencies are necessary to run Clinica. Please refer to this page to determine which third-party libraries you need to install.

Example

Diagram illustrating the Clinica pipelines involved when performing a group comparison of FDG PET data projected on the cortical surface between patients with Alzheimer's disease and healthy controls from the ADNI database:

ClinicaExample

Clinical and neuroimaging data are downloaded from the ADNI website and data are converted into BIDS with the adni-to-bids converter.
Estimation of the cortical and white surface is then produced by the t1-freesurfer pipeline.
FDG PET data can be projected on the subject’s cortical surface and normalized to the FsAverage template from FreeSurfer using the pet-surface pipeline.
TSV file with demographic information of the population studied is given to the statistics-surface pipeline to generate the results of the group comparison.

For more examples and details, please refer to the Documentation.

Support

Check for past answers in the old Clinica Google Group
Start a discussion on Github
Report an issue on GitHub

Contributing

We encourage you to contribute to Clinica! Please check out the Contributing to Clinica guide for guidelines about how to proceed. Do not hesitate to ask questions if something is not clear for you, report an issue, etc.

License

This software is distributed under the MIT License. See license file for more information.

Citing us

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 Frontiers in Neuroinformatics, 2021 doi:10.3389/fninf.2021.689675

Related Repositories

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: 1.2.0
message: If you use this software, please cite it as below.
authors:
  - family-names: Routier
    given-names:  Alexandre
  - family-names: Burgos
    given-names: Ninon
  - family-names: Diaz
    given-names: Mauricio
  - family-names: Bacci
    given-names: Michael
  - family-names: Bottani
    given-names: Simona
  - family-names: El-Rifai
    given-names: Omar
  - family-names: Fontanella
    given-names: Sabrina
  - family-names: Gori
    given-names: Pietro
  - family-names: Guillon
    given-names: Jérémy
  - family-names: Guyot
    given-names: Alexis
  - family-names: Hassanaly
    given-names: Ravi
  - family-names: Jacquemont
    given-names: Thomas
  - family-names: Lu
    given-names: Pascal
  - family-names: Marcoux
    given-names: Arnaud
  - family-names: Moreau
    given-names: Tristan
  - family-names: Samper-Gonzalez
    given-names: Jorge
  - family-names: Teichmann
    given-names: Marc
  - family-names: Thibeau-Sutre
    given-names: Elina
  - family-names: Vaillant
    given-names: Ghislain
  - family-names: Wen
    given-names: Junhao
  - family-names: Wild
    given-names: Adam
  - family-names: Habert
    given-names: Marie-Odile
  - family-names: Durrleman
    given-names: Stanley
  - family-names: Colliot
    given-names: Olivier
title: "Clinica: An Open Source Software Platform for Reproducible Clinical Neuroscience Studies"
doi: 10.3389/fninf.2021.689675
license: MIT

GitHub Events

Total

Create event: 8
Release event: 5
Issues event: 148
Watch event: 25
Delete event: 4
Member event: 1
Issue comment event: 274
Push event: 108
Pull request review comment event: 236
Pull request review event: 274
Pull request event: 233
Fork event: 13

Last Year

Create event: 8
Release event: 5
Issues event: 148
Watch event: 25
Delete event: 4
Member event: 1
Issue comment event: 274
Push event: 108
Pull request review comment event: 236
Pull request review event: 274
Pull request event: 233
Fork event: 13

Committers

Last synced: 7 months ago

All Time

Total Commits: 3,245
Total Committers: 55
Avg Commits per committer: 59.0
Development Distribution Score (DDS): 0.786

Past Year

Commits: 177
Committers: 12
Avg Commits per committer: 14.75
Development Distribution Score (DDS): 0.537

Top Committers

Name	Email	Commits
Alexandre Routier	a**r@g**m	693
Mauricio DIAZ	m**z@i**r	476
Gensollen	n**n@g**m	286
Nono	a**x@i**r	273
Hao	a**6@h**m	218
Ghislain Vaillant	g****l	208
Jérémy Guillon	j**n@i**r	132
jsampergonzalez	j**z@g**m	128
AliceJoubert	1****t	106
Sabrina Fontanella	s**a@i**g	100
omar-rifai	o**d@g**m	96
michael.bacci	m**i@i**r	73
simonabottani	s**2@g**m	71
Matthieu Joulot	8****t	63
dependabot[bot]	4****]	35
Pietro Gori	p**i@i**r	34
Elina Thibeau Sutre	e**e@i**g	34
BOTTANI Simona	s**i@u**g	33
GUYOT Alexis	a**t@U**g	27
Thomas Jacquemont	t**t@e**r	24
BOTTANI Simona	s**i@i**g	17
Ninon Burgos	n**s@i**r	17
Thomas JACQUEMONT (Olivier COLLIOT)	j**t@H**)	12
Adam ISMAILI	1****2	11
Pascal	p**u@i**g	10
Ravi Hassanaly	4****8	9
Ninon Burgos	n**s@g**m	9
Elina Thibeau Sutre	e**s@f**r	7
adamwild	a**d@e**g	4
Ana Fouquier	a**g@g**m	3
and 25 more...

Committer Domains (Top 20 + Academic)

icm-institute.org: 6 inria.fr: 6 umr-arami-lf002.icm-institute.org: 2 umr-arami-mp008.icm-institute.org: 1 umr-arami-mp021.icm-institute.org: 1 umr-arami-lf001.icm-institute.org: 1 onerussian.com: 1 umr-arami-mp017.icm-institute.org: 1 umr-cogim-mp014.icm-institute.org: 1 upmc.fr: 1 ensta-bretagne.org: 1 free.fr: 1 hp2c23.(none): 1 ens.fr: 1 umr-arami-mp004.icm-institute.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 208
Total pull requests: 679
Average time to close issues: 3 months
Average time to close pull requests: 16 days
Total issue authors: 47
Total pull request authors: 24
Average comments per issue: 2.68
Average comments per pull request: 0.49
Merged pull requests: 551
Bot issues: 0
Bot pull requests: 40

Past Year

Issues: 90
Pull requests: 182
Average time to close issues: 20 days
Average time to close pull requests: 6 days
Issue authors: 19
Pull request authors: 16
Average comments per issue: 0.63
Average comments per pull request: 0.49
Merged pull requests: 130
Bot issues: 0
Bot pull requests: 2

View more stats

Top Authors

Issue Authors

NicolasGensollen (75)
AliceJoubert (42)
omar-rifai (15)
ghisvail (7)
MatthieuJoulot (7)
fyb99 (7)
souravraha (6)
espentrydal (3)
AudreyDuran (3)
mtmmu88 (3)
ta4218 (2)
ravih18 (2)
Luoyu-Wang (2)
manonheff (1)
J-V1 (1)

Pull Request Authors

NicolasGensollen (381)
AliceJoubert (144)
dependabot[bot] (40)
ghisvail (39)
MatthieuJoulot (26)
Adam-Ismaili-92 (11)
HuguesRoy (6)
14thibea (6)
ravih18 (5)
yarikoptic (4)
mdiazmel (2)
camillebrianceau (2)
likeajumprope (2)
msolal (1)
maylistran01 (1)

Top Labels

Issue Labels

bug (82) enhancement (46) converter (45) doc (32) inactive (20) good first issue (17) pipeline (11) CI (7) dependencies (5) iotools (2) duplicate (1) wontfix (1) question (1)

Pull Request Labels

converter (78) fix (68) doc (48) dependencies (47) enhancement (41) python (40) CI (37) pipeline (29) Stale (19) github_actions (10) bug (6) iotools (3) good first issue (1)

Packages

Total packages: 1
Total downloads:
- pypi 702 last-month

Total dependent packages: 1
Total dependent repositories: 1
Total versions: 48
Total maintainers: 4

pypi.org: clinica

Software platform for clinical neuroimaging studies

Homepage: https://www.clinica.run
Documentation: https://aramislab.paris.inria.fr/clinica/docs/public/latest
License: MIT
Latest release: 0.10.1
published 7 months ago

Versions: 48
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 702 Last month

Rankings

Dependent packages count: 4.8%

Stargazers count: 5.0%

Forks count: 5.4%

Average: 9.3%

Downloads: 10.0%

Dependent repos count: 21.5%

Maintainers (4)

aramis ghisvail NicolasGensollen mdiaz

Last synced: 7 months ago

Dependencies

poetry.lock pypi

112 dependencies

pyproject.toml pypi

black * develop
isort * develop
nipy ^0.5.0 develop
pre-commit * develop
pytest * develop
pytest-cov ^3.0.0 develop
pytest-timeout * develop
pytest-xdist * develop
argcomplete ^1.9.4
attrs >=20.1.0
cattrs ^1.9.0
click ^8
click-option-group ^0.5
colorlog ^5
fsspec *
jinja2 ^3
matplotlib *
mkdocs ^1.1
mkdocs-material >=7.1.8
networkx *
nibabel ^2.3.3
niflow-nipype1-workflows *
nilearn ^0.7.0
nipype ^1.7.1
numpy ^1.17
openpyxl *
pandas ^1.2
pybids ^0.15.1
pydicom *
pydra ^0.18
pydra-nipype1 ^0.1.0
pymdown-extensions *
python >=3.8,<3.11
scikit-image ^0.19
scikit-learn ^1.0
scipy ^1.7
xgboost *
xlrd *
xvfbwrapper *

.github/workflows/lint.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
snok/install-poetry v1 composite

.github/workflows/publish.yaml actions

actions/checkout v3 composite
snok/install-poetry v1 composite

.github/workflows/stale.yaml actions

actions/stale v7 composite

.github/workflows/test.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
snok/install-poetry v1 composite

environment.yml pypi

clinica

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Clinica

About The Project

Getting Started

Using pipx (recommended)

Using pip

Using Conda

Additional dependencies (required)

Example

Support

Contributing

License

Citing us

Related Repositories

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

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: clinica

Rankings

Maintainers (4)

Dependencies