Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies

Area of Science:

• Clinical neuroscience
• Neuroimaging analysis
• Computational neuroscience

Background:

• Clinical neuroscience studies generate complex multimodal data.
• Reproducibility and data sharing are significant challenges in the field.
• Current tools often lack integrated pipelines for diverse neuroimaging data types.

Purpose of the Study:

• To introduce Clinica, an open-source software platform.
• To simplify data management, processing, and analysis in clinical neuroscience.
• To enhance reproducibility and facilitate data sharing for researchers.

Main Methods:

• Clinica utilizes automatic pipelines for processing multimodal neuroimaging data (T1 MRI, diffusion MRI, PET).
• It supports data organization using the Brain Imaging Data Structure (BIDS) and processed data using the ClinicA Processed Structure (CAPS).
• Includes tools for statistics, machine learning, and deep learning, integrating with existing community tools.

Main Results:

• Provides standardized processing of neuroimaging data into various formats (scalar fields, meshes).
• Facilitates execution of single and sequential pipelines for consistent analysis.
• Enables integration of processed data into statistical and machine learning frameworks.

Conclusions:

• Clinica offers a robust solution for reproducible clinical neuroscience research.
• The platform reduces data management overhead and improves analysis efficiency.
• It supports collaboration through standardized data and results sharing.