Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal QC, Canada.
Front Neuroinform. 2012 Apr 3;6:7. doi: 10.3389/fninf.2012.00007. eCollection 2012.
The analysis of neuroimaging databases typically involves a large number of inter-connected steps called a pipeline. The pipeline system for Octave and Matlab (PSOM) is a flexible framework for the implementation of pipelines in the form of Octave or Matlab scripts. PSOM does not introduce new language constructs to specify the steps and structure of the workflow. All steps of analysis are instead described by a regular Matlab data structure, documenting their associated command and options, as well as their input, output, and cleaned-up files. The PSOM execution engine provides a number of automated services: (1) it executes jobs in parallel on a local computing facility as long as the dependencies between jobs allow for it and sufficient resources are available; (2) it generates a comprehensive record of the pipeline stages and the history of execution, which is detailed enough to fully reproduce the analysis; (3) if an analysis is started multiple times, it executes only the parts of the pipeline that need to be reprocessed. PSOM is distributed under an open-source MIT license and can be used without restriction for academic or commercial projects. The package has no external dependencies besides Matlab or Octave, is straightforward to install and supports of variety of operating systems (Linux, Windows, Mac). We ran several benchmark experiments on a public database including 200 subjects, using a pipeline for the preprocessing of functional magnetic resonance images (fMRI). The benchmark results showed that PSOM is a powerful solution for the analysis of large databases using local or distributed computing resources.
神经影像学数据库的分析通常涉及许多相互连接的步骤，这些步骤被称为流水线。 Octave 和 Matlab 的流水线系统（PSOM）是一种灵活的框架，用于以 Octave 或 Matlab 脚本的形式实现流水线。 PSOM 没有引入新的语言结构来指定工作流程的步骤和结构。 相反，分析的所有步骤都由常规的 Matlab 数据结构描述，记录它们相关的命令和选项，以及它们的输入、输出和清理后的文件。 PSOM 执行引擎提供了许多自动化服务：（1）只要作业之间的依赖关系允许并且有足够的资源可用，它就可以在本地计算设施上并行执行作业；（2）它生成流水线阶段和执行历史的综合记录，该记录详细到足以完全重现分析；（3）如果多次启动分析，它只执行需要重新处理的部分流水线。 PSOM 是根据开源 MIT 许可证分发的，可以无限制地用于学术或商业项目。 该软件包除了 Matlab 或 Octave 之外没有外部依赖项，安装简单，支持多种操作系统（Linux、Windows、Mac）。 我们在一个包含 200 个受试者的公共数据库上运行了几个基准实验，使用了一个用于功能磁共振成像（fMRI）预处理的流水线。 基准测试结果表明，PSOM 是使用本地或分布式计算资源分析大型数据库的强大解决方案。
