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.
The development of Clinica was initiated by the ARAMIS Lab at the Paris Brain Institute.
• 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, NIFD) to BIDS.
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.
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.
Clinica is written in Python. It uses Nipype for pipelining and combines widely-used software packages for neuroimaging data analysis (SPM, FSL, FreeSurfer, MRtrix, ...), machine learning (Scikit-learn) and the BIDS standard for data organization.
Its deep learning companion, ClinicaDL, relies on PyTorch.
Framework for the reproducible processing of neuroimaging data with deep learning
Deep learning classification from brain MRI: Application to Alzheimer’s disease
Framework for the reproducible evaluation of deep learning classification experiments using anatomical MRI data for the computer-aided diagnosis of Alzheimer's disease
Framework for the reproducible evaluation of machine learning classification experiments using anatomical MRI and PET data for the computer-aided diagnosis of Alzheimer's disease
If you are using Clinica, please cite:
Depending on the tools you are using, we may ask you to cite one or several of the following papers:
The papers that should be cited are mentioned in the "Describing this pipeline in your paper" section in the documentation of each pipeline.
Former members of the Clinica team appear in italics.
• Project coordinator
• Co-founder
• Co-founder
• Project coordinator
• Lead developer
• Software architecture
• Optimizations
• Command-line system
• Test / Benchmarks / Profiling
• Atlas-based measurements
• Machine learning
• Dataset converters
• Deep Learning
• Software architecture
• Optimizations
• Continuous integration
• Test / Benchmarks / Profiling
• Software architecture
• Optimizations
• Continuous integration
• Test / Benchmarks / Profiling
• I/O tools
• Dataset converters
• Data structure specifications
• Diffusion MRI analysis
• Software Architecture
• Optimizations
• Functional MRI analysis
• Diffusion MRI analysis
• Anatomical MRI analysis
• Longitudinal analysis
• Shape analysis with Deformetrica
• Test / Benchmarks / Profiling
• PET data analysis
• Deep learning
• Diffusion MRI analysis
• Atlas-based measurements
• Dataset converters
• Anatomical MRI analysis
• Machine learning
• Software Architecture
• Continuous integration
• PET data analysis
• Longitudinal analysis
• Test / Benchmarks / Profiling
• Diffusion MRI analysis
• Software Architecture
• Anatomical MRI analysis
• Diffusion MRI analysis
• Surface-based statistics
• Longitudinal analysis
• CAPS data structure specifications
• Project management
• Documentation
• Website
• Test / Benchmarks / Profiling
• Anatomical MRI analysis
• PET data analysis
• Machine learning
• Dataset converters
• Test / Benchmarks / Profiling
• I/O tools
• Dataset converters
• Deep learning
• ClinicaCloud
• Software architecture
• Optimizations
• Test / Benchmarks / Profiling
• Anatomical MRI analysis
• Diffusion MRI analysis
• Surface-based statistics
• Machine learning
• Deep learning
• Test / Benchmarks / Profiling
• Dataset converters
The ARAMIS Lab is a pluridisciplinary group bringing together methodological researchers (computer science, applied mathematics) and medical experts (neurology, medical imaging).
Institut du Cerveau - Paris Brain Institute
Équipe Aramis, 3eme étage
Hôpital de la Pitié-Salpêtrière
47, boulevard de l’hôpital
75013 Paris
France
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