Implementation of Automated Pipeline for Resting-State fMRI Analysis with PACS Integration

In recent years, the quantity and complexity of medical imaging acquisition and processing have increased tremendously. The explosion in volume and need for advanced imaging analysis have led to the creation of numerous software programs, which have begun to be incorporated into clinical practice for indications such as automated stroke assessment, brain tumor perfusion processing, and hippocampal volume analysis. Despite these advances, there remains a need for specialized, custom-built software for advanced algorithms and new areas of research that is not widely available or adequately integrated in these out-of-the-box solutions. The purpose of this paper is to describe the implementation of an image-processing pipeline that is versatile and simple to create, which allows for rapid prototyping of image analysis algorithms and subsequent testing in a clinical environment. This pipeline uses a combination of Orthanc server, custom MATLAB code, and publicly available FMRIB Software Library and RestNeuMap tools to automatically receive and analyze resting-state functional MRI data collected from a custom filter on the MR scanner output. The processed files are then sent directly to Picture Archiving and Communications System (PACS) without the need for user input. This initial experience can serve as a framework for those interested in simple implementation of an automated pipeline customized to clinical needs.

Automated summary

In recent years, there has been a significant increase in the quantity and complexity of medical imaging acquisition and processing. Although there are numerous software programs available for clinical practice, there is still a need for specialized, custom-built software for advanced algorithms and new research areas. This paper describes the implementation of a versatile and simple image-processing pipeline for rapid prototyping and testing of image analysis algorithms in a clinical environment. The pipeline combines Orthanc server, custom MATLAB code, and publicly available software tools to automatically receive and analyze resting-state functional MRI data.