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Clinica

Software platform for clinical neuroimaging studies

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

Clinica is developed by the ARAMIS Lab at the ICM in Paris.

What are the main features of Clinica?

• Complex processing pipelines involving different software packages.
• Integration between feature extraction and statistics / machine learning.
• Standardized input/output data structures.
• Conversion of publicly available datasets (ADNI, AIBL, OASIS) to BIDS.

Why should I install Clinica?

In short: to make your life easier!

With Clinica you can:
• easily share data and results within your institution and with external collaborators;
• make your research more reproducible;
• spend less time on data management and processing.

Who are the intended users of Clinica?

Clinica is meant for users looking for a straightforward and efficient way to process and analyze neuroimaging data, such as machine learning experts wishing to work with neuroimages or clinical fellows not familiar with image processing and analysis tools.

Which technologies underlie Clinica?

Clinica is written in Python.

It uses the Nipype system for pipelining and combines widely-used software packages for neuroimaging data analysis (SPM, FSL,  FreeSurferMRtrix, ...), machine learning (Scikit-learn) and the BIDS standard for data organization.

  • A. Bertrand, J. Wen, D. Rinaldi, M. Houot, S. Sayah, A. Camuzat, C. Fournier, S. Fontanella, A. Routier, P. Couratier, F. Pasquier, M-O. Habert, D. Hannequin, O. Martinaud, P. Caroppo, R. Levy, B. Dubois, A. Brice, S. Durrleman, O. Colliot, I. Le Ber for the PREV-DEMALS Study Group Early Cognitive, Structural, and Microstructural Changes in Presymptomatic C9orf72 Carriers Younger Than 40 Years. JAMA Neurology, 2017. Access the paper!
  • T. Jacquemont, F. De Vico Fallani, A. Bertrand, S. Epelbaum, A. Routier, B. Dubois, H. Hampel, S. Durrleman, O. Colliot - Amyloidosis and neurodegeneration result in distinct structural connectivity patterns in mild cognitive impairment. Neurobiology of Aging, 2017. Access the paper!
  • N. Burgos, J. Samper-González, A. Bertrand, M-O. Habert, S. Ourselin, S. Durrleman, M. J. Cardoso, O. ColliotIndividual Analysis of Molecular Brain Imaging Data Through Automatic Identification of Abnormality Patterns. Computational Methods for Molecular Imaging - MICCAI 2017 Satellite Workshop, 2017. Access the paper!    
  • J. Samper-Gonzalez, N. Burgos, F. Sabrina, H. Bertin, M-O. Habert, S. Durrleman, T. Evgeniou, O. ColliotYet Another ADNI Machine Learning Paper? Paving The Way Towards Fully-reproducible Research on Classification of Alzheimer's Disease. Machine Learning in Medical Imaging - MICCAI 2017 Satellite Workshop, 2017. Access the paper!
  • Many more to come!

Mobirise

Olivier Colliot

• Project coordinator
• Co-founder

Mobirise

Stanley Durrleman

• Co-founder

Mobirise

Michael Bacci

• Software Architecture
• Optimizations
• Command-line System
• Test / Benchmarks / Profiling

Mobirise

Simona Bottani

• Atlas-based measurements
• Machine learning
• Data converters (AIBL)

Mobirise

Ninon Burgos

• PET data analysis
• Test / Benchmarks / Profiling
• Project management
• Documentation

Mobirise

Sabrina Fontanella

• I/O
• Data converters (ADNI, AIBL, OASIS)
• Data structure specifications

Mobirise

Pietro Gori

• Approximation of white matter bundles (future release)

Mobirise

Jérémy Guillon

• Software Architecture
• Optimizations
• Functional MRI analysis

Mobirise

Thomas Jacquemont

• Diffusion MRI analysis
• Atlas-based measurements

Mobirise

Pascal Lu

• Genetic data analysis (future release)
• Machine learning

Mobirise

Arnaud Marcoux

• PET data analysis
• Test / Benchmarks / Profiling

Mobirise

Tristan Moreau

• Diffusion MRI analysis

Alexandre Routier

Alexandre Routier

• Software Architecture
• Anatomical MRI analysis
• Diffusion MRI analysis
• Surface-based statistics
• CAPS data structure specifications
• Project management
• Documentation
• Website
• Test / Benchmarks / Profiling

Mobirise

Jorge Samper-Gonzalez

• Anatomical MRI analysis
• PET data analysis
• Machine learning
• Data converters (ADNI)
• Test / Benchmarks / Profiling

Mobirise

Junhao Wen

• Anatomical MRI analysis
• Surface-based statistics
• Test / Benchmarks / Profiling

Clinica is a software for research studies.
It is not intended for use in medical routine.

About ARAMIS Lab

ARAMIS Lab is a pluridisciplinary group bringing together methodological researchers (computer science, applied mathematics) and medical experts (neurology, medical imaging).

Address

ICM
Équipe Aramis, 3eme étage
Hôpital de la Pitié-Salpêtrière
47, boulevard de l’hôpital
75013 Paris
France

Support

Mobirise

Copyright (c) 2016-2018 Clinica