Background

Processing and quantitative analysis of magnetic resonance spectroscopy (MRS) data are far from standardized and require interfacing with third-party software. Here, we present Osprey, a fully integrated open-source data analysis pipeline for MRS data, with seamless integration of pre-processing, linear-combination modelling, quantification, and data visualization.

New Method

Osprey loads multiple common MRS data formats, performs phased-array coil combination, frequency-and phase-correction of individual transients, signal averaging and Fourier transformation. Linear combination modelling of the processed spectrum is carried out using simulated basis sets and a spline baseline. The MRS voxel is coregistered to an anatomical image, which is segmented for tissue correction and quantification is performed based upon modelling parameters and tissue segmentation. The results of each analysis step are visualized in the Osprey GUI. The analysis pipeline is demonstrated in 12 PRESS, 11 MEGA-PRESS, and 8 HERMES datasets acquired in healthy subjects.

Results

Osprey successfully loads, processes, models, and quantifies MRS data acquired with a variety of conventional and spectral editing techniques.

Comparison with Existing Method(s)

Osprey is the first MRS software to combine uniform pre-processing, linear-combination modelling, tissue correction and quantification into a coherent ecosystem. Compared to existing compiled, often closed-source modelling software, Osprey’s open-source code philosophy allows researchers to integrate state-of-the-art data processing and modelling routines, and potentially converge towards standardization of analysis.

Conclusions

Osprey combines robust, peer-reviewed data processing methods into a modular workflow that is easily augmented by community developers, allowing the rapid implementation of new methods.

中文翻译：

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Osprey：磁共振波谱数据的开源处理、重建和估计。

背景

磁共振波谱 (MRS) 数据的处理和定量分析远未标准化，需要与第三方软件接口。在这里，我们展示了 Osprey，一个完全集成的 MRS 数据开源数据分析管道，无缝集成了预处理、线性组合建模、量化和数据可视化。

新方法

Osprey 加载多种常见的 MRS 数据格式，执行相控阵线圈组合、单个瞬态的频率和相位校正、信号平均和傅立叶变换。使用模拟基组和样条基线对处理后的光谱进行线性组合建模。MRS 体素被配准到解剖图像，该图像被分割用于组织校正和量化是基于建模参数和组织分割来执行的。每个分析步骤的结果都在 Osprey GUI 中可视化。在健康受试者中获得的 12 个 PRESS、11 个 MEGA-PRESS 和 8 个 HERMES 数据集展示了分析管道。

结果

Osprey 成功加载、处理、建模和量化使用各种传统和光谱编辑技术获取的 MRS 数据。

与现有方法的比较

Osprey 是第一个将统一的预处理、线性组合建模、组织校正和量化结合到一个连贯的生态系统中的 MRS 软件。与现有的已编译的、通常是闭源的建模软件相比，Osprey 的开源代码理念使研究人员能够集成最先进的数据处理和建模例程，并有可能向分析标准化方向发展。

结论

Osprey 将强大的、经过同行评审的数据处理方法结合到一个模块化的工作流程中，社区开发人员可以轻松地对其进行扩充，从而可以快速实施新方法。