Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies.,Frontiers in Neuroinformatics

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Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies.
Frontiers in Neuroinformatics ( IF 3.5 ) Pub Date : 2021-08-13 , DOI: 10.3389/fninf.2021.689675
Alexandre Routier _{1,

2,

3,

4,

5,

6} , Ninon Burgos _{1,

2,

3,

4,

5,

6} , Mauricio Díaz ₇ , Michael Bacci _{1,

2,

3,

4,

5,

6} , Simona Bottani _{1,

2,

3,

4,

5,

6} , Omar El-Rifai _{1,

2,

3,

4,

5,

6} , Sabrina Fontanella _{1,

2,

3,

4,

5,

6} , Pietro Gori _{1,

2,

3,

4,

5,

6} , Jérémy Guillon _{1,

2,

3,

4,

5,

6} , Alexis Guyot _{1,

2,

3,

4,

5,

6} , Ravi Hassanaly _{1,

2,

3,

4,

5,

6} , Thomas Jacquemont _{1,

2,

3,

4,

5,

6} , Pascal Lu _{1,

2,

3,

4,

5,

6} , Arnaud Marcoux _{1,

2,

3,

4,

5,

6} , Tristan Moreau _{2,

3,

4,

5,

6} , Jorge Samper-González _{1,

2,

3,

4,

5,

6} , Marc Teichmann _{2,

3,

4,

5,

6,

8} , Elina Thibeau-Sutre _{1,

2,

3,

4,

5,

6} , Ghislain Vaillant _{1,

2,

3,

4,

5,

6} , Junhao Wen _{1,

2,

3,

4,

5,

6} , Adam Wild _{1,

2,

3,

4,

5,

6} , Marie-Odile Habert _{9,

10,

11} , Stanley Durrleman _{1,

2,

3,

4,

5,

6} , Olivier Colliot _{1,

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6}

Affiliation

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.

中文翻译：

Clinica：用于可重复临床神经科学研究的开源软件平台。

我们展示了 Clinica (www.clinica.run)，这是一个开源软件平台，旨在使临床神经科学研究更容易、更具可重复性。Clinica 旨在让研究人员 (i) 在数据管理和处理上花费更少的时间，(ii) 对其方法进行可重复的评估，以及 (iii) 在其机构内以及与外部合作者轻松共享数据和结果。Clinica 的核心是一组用于处理和分析多模态神经影像数据（目前为 T1 加权 MRI、扩散 MRI 和 PET 数据）的自动管道，以及用于统计、机器学习和深度学习的工具。它依赖于大脑成像数据结构 (BIDS) 来组织原始神经成像数据集，并依赖于社区编写的已建立的工具来构建其管道。它还提供公共神经影像数据集到 BIDS（目前为 ADNI、AIBL、OASIS 和 NIFD）的转换器。处理后的数据包括图像值标量场（例如，组织概率图）、网格、基于表面的标量场（例如，皮质厚度图）或标量输出（例如，区域平均值）。这些数据遵循与 BIDS 具有相同理念的 ClinicA 处理结构 (CAPS) 格式。原始和处理过的神经影像文件的一致组织促进了单个管道和管道序列的执行，以及将处理过的数据集成到统计或机器学习框架中。Clinica 的目标受众是进行涉及多模态成像的临床神经科学研究的神经科学家或临床医生，

更新日期：2021-08-13

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