The open-source neuroimaging research enterprise

Daniel S. Marcus, Kevin A. Archie, Timothy R. Olsen, Mohana Ramaratnam

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

While brain imaging in the clinical setting is largely a practice of looking at images, research neuroimaging is a quantitative and integrative enterprise. Images are run through complex batteries of processing and analysis routines to generate numeric measures of brain characteristics. Other measures potentially related to brain function - demographics, genetics, behavioral tests, neuropsychological tests - are key components of most research studies. The canonical scanner - PACS - viewing station axis used in clinical practice is therefore inadequate for supporting neuroimaging research. Here, we model the neuroimaging research enterprise as a workflow. The principal components of the workflow include data acquisition, data archiving, data processing and analysis, and data utilization. We also describe a set of open-source applications to support each step of the workflow and the transitions between these steps. These applications include DIGITAL IMAGING AND COMMUNICATIONS IN MEDICINE viewing and storage tools, the EXTENSIBLE NEUROIMAGING ARCHIVE TOOLKIT data archiving and exploration platform, and an engine for running processing/analysis pipelines. The overall picture presented is aimed to motivate open-source developers to identify key integration and communication points for interoperating with complimentary applications.

Original languageEnglish
Pages (from-to)130-138
Number of pages9
JournalJournal of Digital Imaging
Volume20
Issue numberSUPPL. 1
DOIs
StatePublished - Nov 2007

Keywords

  • Biomedical imaging
  • DICOM
  • Neuroimaging
  • Neuroinformatics
  • Research workflow
  • XNAT

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