MrSPA: Integrated tools and development platform for magnetic resonance research

描述（由申请人提供）：我们建议更新和扩展三个磁共振波谱（MRS）软件工具，这些工具已被MRS研究界广泛使用了十多年。通过将它们合并到一个集成的、开源的、开放的开发研究平台中，我们将解决它们各自的一些局限性。目前的软件工具为频谱模拟、RF脉冲设计和频谱数据分析提供了资源（分别为加瓦/GAMMA、MatPulse和VeSPA程序）。该研究平台将被称为MrSPA（磁共振仿真、脉冲设计和分析）。临床MRS研究设计包括：1）研究问题，2）针对特定数据采集的脉冲序列重新设计，以及3）稳健的频谱处理和数据分析。将这三个程序合并为一个集成的开发平台将有助于所有三个步骤。使用开放式开发模式和当前的“最佳编程实践”来实施，将降低用户和开发人员的初始学习曲线，并将鼓励快速的新开发。本提案第一部分的目标将侧重于将最初的方案统一和整合为一个一揽子方案。这一过程将解决当前软件的一些局限性，包括：非标准数据访问、使算法扩展和比较复杂化的封闭源多语言软件、共享先前信息的程序之间缺乏集成以及文档和教育内容不完整或缺失。本提案后半部分的目标是通过分布式计算选项、即插即用可扩展性和网络数据共享在全球范围内扩展开发平台功能，并在每个模块中使用特定的工具和算法。软件将在网上免费提供。我们将为当前程序的用户社区提供并支持一个简单的过渡途径。我们将与NIPY联盟（Python中的NeuroImaging）合作，提供行业标准的开放式开发工具，并为用户提供易于安装的软件包，并为开发人员提供源代码存储库访问。公共卫生相关性：该提案将更新和扩展现有的三个磁共振波谱（MRS）软件工具，将它们合并到一个单一的综合研究平台。MRS是一种强有力的非侵入性工具，用于在体内和体外定量代谢物变化，而无需使用电离辐射。MRS作为临床研究工具的重要性在于其检测仅表现出非特异性MR成像（MRI）结果时可能观察到的疾病特异性变化或在不存在单独使用MRI观察到的结构异常时可能发生的代谢变化的潜力。它已在临床上应用于正常衰老、创伤性脑损伤、多发性硬化症、阿尔茨海默病、癫痫和脑肿瘤评估，仅举几例，并且在动物和体外实验中应用的范围甚至更广。在过去的十年中，由于支持更高磁场MR扫描仪的必要技术的快速发展以及各种MR数据采集方案的巨大进步，临床MRS研究经历了巨大的增长。将这三种MRS工具合并到一个综合平台中，将促进和鼓励使用综合的MRS研究设计，这些设计将数据采集和分析的所有步骤结合起来，以调查具体的研究问题。

DESCRIPTION (provided by applicant): We propose to update and expand upon three magnetic resonance spectroscopy (MRS) software tools that have been used extensively by the MRS research community for over a decade. By merging them into an integrated, open source, open development research platform, we will address a number of their individual limitations. The current software tools provide resources for spectral simulation, RF pulse design and spectral data analysis (GAVA/GAMMA, MatPulse and VeSPA programs, respectively). The proposed research platform will be called MrSPA (Magnetic Resonance Simulation, Pulse design and Analysis). Clinical MRS research design encompasses: 1) the research question, 2) pulse sequence re-design for specific data acquisition, and 3) robust spectral processing and data analysis. Amalgamation of the three programs into an integrated development platform will facilitate all three steps. Implementation using an open development model and current "best programming practices" will lower the initial learning curve for users and developers, and will encourage rapid new development. The aims of the first part of this proposal will focus on the unification and integration of the initial programs into one package. This process will address a number of limitations of the current software including: non-standard data access, closed source multiple language software that complicates algorithm extension and comparison, lack of integration between programs for sharing prior information, and incomplete or missing documentation and educational content. The aims of the second half of this proposal will expand the development platform functionality both globally, via distributed computing options, plug-and-play extensibility, and networked data sharing; and also in each module with specific tools and algorithms. Software will be made available online for free. We will provide and support a simple transition pathway for the user communities of the current programs. We will partner with the NIPY consortium (NeuroImaging in Python) to provide industry standard open development tools and to facilitate dissemination of both easy to install packages for users and for source code repository access for developers. PUBLIC HEALTH RELEVANCE: This proposal will update and expand upon three existing magnetic resonance spectroscopy (MRS) software tools by merging them into a single integrated research platform. MRS is a powerful non-invasive tool for quantifying metabolite changes both in vivo and in vitro without the use of ionizing radiation. The importance of MRS as a clinical investigation tool is its potential to detect disease specific changes that may be observed where only non-specific MR imaging (MRI) findings are manifested or metabolic changes that may occur in the absence of structural abnormalities seen using MRI alone. It has found applications clinically in normal aging, traumatic brain injury, multiple sclerosis, Alzheimer's disease, epilepsy and brain tumor evaluation, to name a few, and an even wider spread of applications in animal and in vitro experiments. Clinical MRS research has experienced a tremendous growth in the last decade, owing to the rapid development of the necessary technology to support higher magnetic field MR scanners, and the great progress made in various MR data acquisition schemes. Merging these three MRS tools into an integrated platform will facilitate and encourage the use of comprehensive MRS research designs that incorporate all steps of data acquisition and analysis to investigate specific research questions.