MrSPA: Integrated tools and development platform for magnetic resonance research

描述(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，它们已经被MRS研究社区广泛使用了十多年。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限制。目前的软件工具为频谱模拟、RF脉冲设计和频谱数据分析(分别为GAVA/伽马、MatPulse和VESPA程序)提供资源。提出的研究平台将被称为MR SPA(磁共振模拟，脉冲设计和分析)。临床MRS研究设计包括：1)研究问题，2)针对特定数据采集重新设计脉冲序列，3)稳健的频谱处理和数据分析。将这三个方案合并为一个综合开发平台将促进所有这三个步骤。使用开放的开发模式和当前的“最佳编程实践”进行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。该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。这一进程将解决当前软件的一些局限性，包括：非标准数据访问、封闭源码多语言软件使算法扩展和比较复杂化、共享先前信息的程序之间缺乏整合、文件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联网数据共享，在全球范围内以及在每个模块中使用特定的工具和算法来扩展开发平台的功能。软件将在网上免费提供。我们将为当前计划的用户社区提供并支持一条简单的过渡途径。我们将与NIPY联盟(Python中的神经成像)合作，提供行业标准的开放开发工具，并为用户提供易于安装的包以及为开发人员提供源代码库访问提供便利。公共卫生相关性：这项提案将更新和扩展现有的三个磁共振波谱(MRS)软件工具，将它们合并为一个单一的综合研究平台。MRS是一种强大的非侵入性工具，可以在不使用电离辐射的情况下对体内和体外的代谢物变化进行量化。MRS作为一种临床研究工具的重要性在于，它有可能检测到只有非特异性磁共振成像(MRI)发现的疾病特异性变化，或者在没有仅使用MRI看到的结构异常的情况下可能发生的代谢变化。它已经在正常衰老、创伤性脑损伤、多发性硬化症、阿尔茨海默病、癫痫和脑肿瘤评估等方面获得了临床应用，并在动物和体外实验中得到了更广泛的应用。在过去的十年里，由于支持更高磁场磁共振扫描仪的必要技术的快速发展，以及各种磁共振数据采集方案的巨大进步，临床磁共振研究经历了巨大的增长。将这三个MRS工具合并到一个综合平台中，将促进和鼓励使用综合MRS研究设计，该设计包含数据获取和分析的所有步骤，以调查特定的研究问题。

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.