Frazier-Logue Noah, Wang Justin, Wang Zheng, Sodums Devin, Khosla Anisha, Samson Alexandria D, McIntosh Anthony R, Shen Kelly
Rotman Research Institute, Baycrest, Toronto, ON, Canada.
Institute for Neuroscience and Neurotechnology, Simon Fraser University, Burnaby, BC, Canada.
Front Neuroinform. 2022 Jun 14;16:883223. doi: 10.3389/fninf.2022.883223. eCollection 2022.
TheVirtualBrain, an open-source platform for large-scale network modeling, can be personalized to an individual using a wide range of neuroimaging modalities. With the growing number and scale of neuroimaging data sharing initiatives of both healthy and clinical populations comes an opportunity to create large and heterogeneous sets of dynamic network models to better understand individual differences in network dynamics and their impact on brain health. Here we present TheVirtualBrain-UK Biobank pipeline, a robust, automated and open-source brain image processing solution to address the expanding scope of TheVirtualBrain project. Our pipeline generates connectome-based modeling inputs compatible for use with TheVirtualBrain. We leverage the existing multimodal MRI processing pipeline from the UK Biobank made for use with a variety of brain imaging modalities. We add various features and changes to the original UK Biobank implementation specifically for informing large-scale network models, including user-defined parcellations for the construction of matching whole-brain functional and structural connectomes. Changes also include detailed reports for quality control of all modalities, a streamlined installation process, modular software packaging, updated software versions, and support for various publicly available datasets. The pipeline has been tested on various datasets from both healthy and clinical populations and is robust to the morphological changes observed in aging and dementia. In this paper, we describe these and other pipeline additions and modifications in detail, as well as how this pipeline fits into the TheVirtualBrain ecosystem.
虚拟大脑（TheVirtualBrain）是一个用于大规模网络建模的开源平台，可使用多种神经成像模式针对个体进行个性化定制。随着健康人群和临床人群神经成像数据共享计划数量的增加和规模的扩大，出现了一个创建大型且异构的动态网络模型集的机会，以便更好地理解网络动力学中的个体差异及其对大脑健康的影响。在此，我们展示了虚拟大脑 - 英国生物银行管道，这是一种强大、自动化且开源的脑图像处理解决方案，以应对虚拟大脑项目不断扩大的范围。我们的管道生成与虚拟大脑兼容的基于连接组的建模输入。我们利用英国生物银行现有的多模态MRI处理管道，该管道适用于各种脑成像模式。我们对英国生物银行的原始实现添加了各种功能和更改，专门用于为大规模网络模型提供信息，包括用于构建匹配的全脑功能和结构连接组的用户定义分区。更改还包括所有模式的详细质量控制报告、简化的安装过程、模块化软件包、更新的软件版本以及对各种公开可用数据集的支持。该管道已在来自健康人群和临床人群的各种数据集上进行了测试，并且对衰老和痴呆中观察到的形态变化具有鲁棒性。在本文中，我们详细描述了这些以及其他管道添加和修改内容，以及该管道如何融入虚拟大脑生态系统。
