title: Development and validation of an open source quantification tool for DSC-MRI studies.
abstract: BACKGROUND
  This work presents the development of an open source tool for the quantification of dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license.
  
  
  METHODS
  This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared.
  
  
  RESULTS
  Perfusion parameters and the corresponding parametric images were obtained. When no gamma-fitting is used, an excellent agreement with the tool used as a gold-standard was obtained (R(2)>0.8 and values are within 95% CI limits in Bland-Altman plots).
  
  
  CONCLUSIONS
  An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license.
authors.affiliation: Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain. Electronic address: pmacias@hggm.es.
authors.forename: P M
authors.initials: PM
authors.lastname: Gordaliza
authors.affiliation: Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain.
authors.forename: J M
authors.initials: JM
authors.lastname: Mateos-Pérez
authors.affiliation: Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain.
authors.forename: P
authors.initials: P
authors.lastname: Montesinos
authors.affiliation: Servicio de Radiodiagnóstico, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
authors.forename: J A
authors.initials: JA
authors.lastname: Guzmán-de-Villoria
authors.affiliation: Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Desco
authors.affiliation: Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain. Electronic address: juanjose.vaquero@uc3m.es.
authors.forename: J J
authors.initials: JJ
authors.lastname: Vaquero
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001921:Brain / Q000473:pathology; D001932:Brain Neoplasms / Q000473:pathology; D038524:Diffusion Magnetic Resonance Imaging / Q000379:methods*; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008297:Male; D008875:Middle Aged; D055420:Perfusion Imaging / Q000379:methods*; D012044:Regression Analysis; D015203:Reproducibility of Results; D012984:Software
keywords: ImageJ; Magnetic resonance imaging; Open source; Perfusion; Software tool