title: An image analysis pipeline for the semi-automated analysis of clinical fMRI images based on freely available software.
abstract: 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.
authors.affiliation: Department of Neurosurgery, The Methodist Hospital, Houston, TX, USA. ckarmonik@tmhs.org
authors.forename: Christof
authors.initials: C
authors.lastname: Karmonik
authors.forename: Michele
authors.initials: M
authors.lastname: York
authors.forename: Robert
authors.initials: R
authors.lastname: Grossman
authors.forename: Ekta
authors.initials: E
authors.lastname: Kakkar
authors.forename: Krutina
authors.initials: K
authors.lastname: Patel
authors.forename: Hani
authors.initials: H
authors.lastname: Haykal
authors.forename: David
authors.initials: D
authors.lastname: King
mesh_terms: D001331:Automation; D007091:Image Processing, Computer-Assisted; D008279:Magnetic Resonance Imaging / Q000379:methods*; D009316:National Institutes of Health (U.S.); D012984:Software; D014481:United States