title: A semi-automated measuring system of brain diffusion and perfusion magnetic resonance imaging abnormalities in patients with multiple sclerosis based on the integration of coregistration and tissue segmentation procedures.
abstract: BACKGROUND
  Diffusion-weighted imaging (DWI) and perfusion-weighted imaging (PWI) abnormalities in patients with multiple sclerosis (MS) are currently measured by a complex combination of separate procedures. Therefore, the purpose of this study was to provide a reliable method for reducing analysis complexity and obtaining reproducible results.
  
  
  METHODS
  We implemented a semi-automated measuring system in which different well-known software components for magnetic resonance imaging (MRI) analysis are integrated to obtain reliable measurements of DWI and PWI disturbances in MS.
  
  
  RESULTS
  We generated the Diffusion/Perfusion Project (DPP) Suite, in which a series of external software programs are managed and harmonically and hierarchically incorporated by in-house developed Matlab software to perform the following processes: 1) image pre-processing, including imaging data anonymization and conversion from DICOM to Nifti format; 2) co-registration of 2D and 3D non-enhanced and Gd-enhanced T1-weighted images in fluid-attenuated inversion recovery (FLAIR) space; 3) lesion segmentation and classification, in which FLAIR lesions are at first segmented and then categorized according to their presumed evolution; 4) co-registration of segmented FLAIR lesion in T1 space to obtain the FLAIR lesion mask in the T1 space; 5) normal appearing tissue segmentation, in which T1 lesion mask is used to segment basal ganglia/thalami, normal appearing grey matter (NAGM) and normal appearing white matter (NAWM); 6) DWI and PWI map generation; 7) co-registration of basal ganglia/thalami, NAGM, NAWM, DWI and PWI maps in previously segmented FLAIR space; 8) data analysis. All these steps are automatic, except for lesion segmentation and classification.
  
  
  CONCLUSIONS
  We developed a promising method to limit misclassifications and user errors, providing clinical researchers with a practical and reproducible tool to measure DWI and PWI changes in MS.
authors.affiliation: Unità Operativa di Neuroradiologia, Dipartimento di Neuroscienze e Riabilitazione, Azienda Ospedaliero-Universitaria of Ferrara, Arcispedale S. Anna, Via Aldo Moro 8, 44124, Cona, Ferrara, Italy. alfredo@revenaz.it.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Revenaz
authors.affiliation: Consiglio Nazionale delle Ricerche, 44124, Ferrara, Italy. m.ruggeri@imamoter.cnr.it.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Ruggeri
authors.affiliation: MR Research Laboratory, IRCCS Don Gnocchi Foundation ONLUS, Milan, Italy. mlagana@dongnocchi.it.
authors.forename: Marcella
authors.initials: M
authors.lastname: Laganà
authors.affiliation: MR Research Laboratory, IRCCS Don Gnocchi Foundation ONLUS, Milan, Italy. niels.bergsland@gmail.com.|Buffalo Neuroimaging Analysis Center, Department of Neurology, University at Buffalo SUNY, Buffalo, NY, USA. niels.bergsland@gmail.com.
authors.forename: Niels
authors.initials: N
authors.lastname: Bergsland
authors.affiliation: Sezione di Neurologia, Dipartimento di Scienze Biomediche e Chirurgico Specialistiche, Università di Ferrara, Ferrara, Italy. grplbt@unife.it.
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Groppo
authors.affiliation: Unità Operativa di Sclerosi Multipla, Fondazione Don Gnocchi ONLUS, IRCCS S. Maria Nascente, 20148, Milano, Italy. mrovaris@dongnocchi.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Rovaris
authors.affiliation: Unità Operativa di Neuroradiologia, Dipartimento di Neuroscienze e Riabilitazione, Azienda Ospedaliero-Universitaria of Ferrara, Arcispedale S. Anna, Via Aldo Moro 8, 44124, Cona, Ferrara, Italy. henryfai@tin.it.
authors.forename: Enrico
authors.initials: E
authors.lastname: Fainardi
mesh_terms: D001921:Brain / Q000473:pathology*; D003952:Diagnostic Imaging / Q000379:methods; D038524:Diffusion Magnetic Resonance Imaging / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D018810:Magnetic Resonance Angiography / Q000379:methods*; D009103:Multiple Sclerosis / Q000473:pathology*; D012984:Software