Frontiers in Neuroinformatics (Aug 2021)

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

  • Alexandre Routier,
  • Alexandre Routier,
  • Alexandre Routier,
  • Alexandre Routier,
  • Alexandre Routier,
  • Alexandre Routier,
  • Ninon Burgos,
  • Ninon Burgos,
  • Ninon Burgos,
  • Ninon Burgos,
  • Ninon Burgos,
  • Ninon Burgos,
  • Mauricio Díaz,
  • Michael Bacci,
  • Michael Bacci,
  • Michael Bacci,
  • Michael Bacci,
  • Michael Bacci,
  • Michael Bacci,
  • Simona Bottani,
  • Simona Bottani,
  • Simona Bottani,
  • Simona Bottani,
  • Simona Bottani,
  • Simona Bottani,
  • Omar El-Rifai,
  • Omar El-Rifai,
  • Omar El-Rifai,
  • Omar El-Rifai,
  • Omar El-Rifai,
  • Omar El-Rifai,
  • Sabrina Fontanella,
  • Sabrina Fontanella,
  • Sabrina Fontanella,
  • Sabrina Fontanella,
  • Sabrina Fontanella,
  • Sabrina Fontanella,
  • Pietro Gori,
  • Pietro Gori,
  • Pietro Gori,
  • Pietro Gori,
  • Pietro Gori,
  • Pietro Gori,
  • Jérémy Guillon,
  • Jérémy Guillon,
  • Jérémy Guillon,
  • Jérémy Guillon,
  • Jérémy Guillon,
  • Jérémy Guillon,
  • Alexis Guyot,
  • Alexis Guyot,
  • Alexis Guyot,
  • Alexis Guyot,
  • Alexis Guyot,
  • Alexis Guyot,
  • Ravi Hassanaly,
  • Ravi Hassanaly,
  • Ravi Hassanaly,
  • Ravi Hassanaly,
  • Ravi Hassanaly,
  • Ravi Hassanaly,
  • Thomas Jacquemont,
  • Thomas Jacquemont,
  • Thomas Jacquemont,
  • Thomas Jacquemont,
  • Thomas Jacquemont,
  • Thomas Jacquemont,
  • Pascal Lu,
  • Pascal Lu,
  • Pascal Lu,
  • Pascal Lu,
  • Pascal Lu,
  • Pascal Lu,
  • Arnaud Marcoux,
  • Arnaud Marcoux,
  • Arnaud Marcoux,
  • Arnaud Marcoux,
  • Arnaud Marcoux,
  • Arnaud Marcoux,
  • Tristan Moreau,
  • Tristan Moreau,
  • Tristan Moreau,
  • Tristan Moreau,
  • Tristan Moreau,
  • Jorge Samper-González,
  • Jorge Samper-González,
  • Jorge Samper-González,
  • Jorge Samper-González,
  • Jorge Samper-González,
  • Jorge Samper-González,
  • Marc Teichmann,
  • Marc Teichmann,
  • Marc Teichmann,
  • Marc Teichmann,
  • Marc Teichmann,
  • Marc Teichmann,
  • Elina Thibeau-Sutre,
  • Elina Thibeau-Sutre,
  • Elina Thibeau-Sutre,
  • Elina Thibeau-Sutre,
  • Elina Thibeau-Sutre,
  • Elina Thibeau-Sutre,
  • Ghislain Vaillant,
  • Ghislain Vaillant,
  • Ghislain Vaillant,
  • Ghislain Vaillant,
  • Ghislain Vaillant,
  • Ghislain Vaillant,
  • Junhao Wen,
  • Junhao Wen,
  • Junhao Wen,
  • Junhao Wen,
  • Junhao Wen,
  • Junhao Wen,
  • Adam Wild,
  • Adam Wild,
  • Adam Wild,
  • Adam Wild,
  • Adam Wild,
  • Adam Wild,
  • Marie-Odile Habert,
  • Marie-Odile Habert,
  • Marie-Odile Habert,
  • Stanley Durrleman,
  • Stanley Durrleman,
  • Stanley Durrleman,
  • Stanley Durrleman,
  • Stanley Durrleman,
  • Stanley Durrleman,
  • Olivier Colliot,
  • Olivier Colliot,
  • Olivier Colliot,
  • Olivier Colliot,
  • Olivier Colliot,
  • Olivier Colliot

DOI
https://doi.org/10.3389/fninf.2021.689675
Journal volume & issue
Vol. 15

Abstract

Read online

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.

Keywords