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

Frontiers in Neuroinformatics

Marie-Odile Habert²  Sabrina Fontanella³  Tristan Moreau³  Adam Wild³  Jérémy Guillon³  Pascal Lu³  Elina Thibeau-Sutre³  Stanley Durrleman³  Alexandre Routier³  Simona Bottani³  Omar El-Rifai³  Michael Bacci³  Pietro Gori³  Arnaud Marcoux³  Ninon Burgos³  Junhao Wen³  Alexis Guyot³  Olivier Colliot³  Ghislain Vaillant³  Thomas Jacquemont³  Jorge Samper-González³  Ravi Hassanaly³  Marc Teichmann⁵  Mauricio Díaz⁷ 

[1] 0AP-HP, Hôpital Pitié-Salpêtrière, Médecine Nucléaire, Paris, France;1Centre d'Acquisition et Traitement des Images, Paris, France;AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France;CNRS, Paris, France;Department of Neurology, Institute for Memory and Alzheimer's Disease, Pitié-Salpêtrière Hospital, AP-HP, Paris, France;Inria, Aramis Project-Team, Paris, France;Inria, Service d'Expérimentation et de Développement, Paris, France;Inserm, Paris, France;Institut du Cerveau – Paris Brain Institute – ICM, Paris, France;Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale (LIB), Paris, France;Sorbonne Université, Paris, France;

关键词: neuroimaging;    software;    pipeline;    data processing and analysis;    machine learning;    multimodal neuroimaging data;   

DOI  :  10.3389/fninf.2021.689675

来源: DOAJ

【 摘 要 】

We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to (i) spend less time on data management and processing, (ii) perform reproducible evaluations of their methods, and (iii) easily share data and results within their institution and with external collaborators. The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI, and PET data), as well as tools for statistics, machine learning, and deep learning. It relies on the brain imaging data structure (BIDS) for the organization of raw neuroimaging datasets and on established tools written by the community to build its pipelines. It also provides converters of public neuroimaging datasets to BIDS (currently ADNI, AIBL, OASIS, and NIFD). Processed data include image-valued scalar fields (e.g., tissue probability maps), meshes, surface-based scalar fields (e.g., cortical thickness maps), or scalar outputs (e.g., regional averages). These data follow the ClinicA Processed Structure (CAPS) format which shares the same philosophy as BIDS. Consistent organization of raw and processed neuroimaging files facilitates the execution of single pipelines and of sequences of pipelines, as well as the integration of processed data into statistics or machine learning frameworks. The target audience of Clinica is neuroscientists or clinicians conducting clinical neuroscience studies involving multimodal imaging, and researchers developing advanced machine learning algorithms applied to neuroimaging data.

【 授权许可】

Unknown