An image analysis pipeline for the semi-automated analysis of clinical fMRI images based on freely available software. Academic Article uri icon



  • The technique of functional Magnetic Resonance Imaging (fMRI) has evolved in the last 15 years from a research concept into a clinically relevant medical procedure. In this study, an efficient, semi-automated and cost-effective solution for the analysis of fMRI images acquired in a clinical setting is presented relying heavily on open source software. The core of the pipeline is the software Analysis of Functional NeuroImages (AFNI, National Institute of Mental Health (NIMH)) combined with K-PACS and ImageJ. Its application is illustrated with clinical fMRI exams and with a research study involving comparing subjects diagnosed with Parkinson's disease and age-matched controls.

publication date

  • January 13, 2010



  • Automation
  • Image Processing, Computer-Assisted
  • Magnetic Resonance Imaging
  • Software


Scopus Document Identifier

  • 77549088511

Digital Object Identifier (DOI)

  • 10.1016/j.compbiomed.2009.12.003

PubMed ID

  • 20074720

Additional Document Info


  • 40


  • 3