Leveraging Open Source/Freeware Tools and Design Methodologies in Translational Research: A Siemens-Based Case Study -- From Raw Diffusion and Structural Data to PACS and the Web

Rudolph Pienaar¹, Ruopeng Wang¹, Bruce Fischl¹, Van Wedeen¹, Patricia Ellen Grant¹

This paper demonstrates a simple and robust method of assembling powerful image processing pipelines based on collections of largely independent image processing tools. These pipelines are open source in nature, and underlying components either open source or freeware. In this study, the pipelines are deployed to a Linux workstation and images collected on Siemens scanners. This Linux workstation can process data directly on the scanner itself, or receive DICOM data from a conventional hospital PACS. Final outputs are automatically parsed for access via the web, or are re-transmitted back to a PACS.