title: From raw data to data-analysis for magnetic resonance spectroscopy--the missing link: jMRUI2XML.
abstract: BACKGROUND
  Magnetic resonance spectroscopy provides metabolic information about living tissues in a non-invasive way. However, there are only few multi-centre clinical studies, mostly performed on a single scanner model or data format, as there is no flexible way of documenting and exchanging processed magnetic resonance spectroscopy data in digital format. This is because the DICOM standard for spectroscopy deals with unprocessed data. This paper proposes a plugin tool developed for jMRUI, namely jMRUI2XML, to tackle the latter limitation. jMRUI is a software tool for magnetic resonance spectroscopy data processing that is widely used in the magnetic resonance spectroscopy community and has evolved into a plugin platform allowing for implementation of novel features.
  
  
  RESULTS
  jMRUI2XML is a Java solution that facilitates common preprocessing of magnetic resonance spectroscopy data across multiple scanners. Its main characteristics are: 1) it automates magnetic resonance spectroscopy preprocessing, and 2) it can be a platform for outputting exchangeable magnetic resonance spectroscopy data. The plugin works with any kind of data that can be opened by jMRUI and outputs in extensible markup language format. Data processing templates can be generated and saved for later use. The output format opens the way for easy data sharing- due to the documentation of the preprocessing parameters and the intrinsic anonymization--for example for performing pattern recognition analysis on multicentre/multi-manufacturer magnetic resonance spectroscopy data.
  
  
  CONCLUSIONS
  jMRUI2XML provides a self-contained and self-descriptive format accounting for the most relevant information needed for exchanging magnetic resonance spectroscopy data in digital form, as well as for automating its processing. This allows for tracking the procedures the data has undergone, which makes the proposed tool especially useful when performing pattern recognition analysis. Moreover, this work constitutes a first proposal for a minimum amount of information that should accompany any magnetic resonance processed spectrum, towards the goal of achieving better transferability of magnetic resonance spectroscopy studies.
authors.affiliation: Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, UAB, Cerdanyola del Vallès, Barcelona, 08193, Spain. victor.mocioiu@uab.cat.|Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina CIBER-BBN, Cerdanyola del Vallès, Barcelona, Spain. victor.mocioiu@uab.cat.|Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain. victor.mocioiu@uab.cat.
authors.forename: Victor
authors.initials: V
authors.lastname: Mocioiu
authors.affiliation: Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina CIBER-BBN, Cerdanyola del Vallès, Barcelona, Spain. S.OrtegaMartorell@ljmu.ac.uk.|School of Computing and Mathematical Sciences, Liverpool John Moores University, Liverpool, UK. S.OrtegaMartorell@ljmu.ac.uk.
authors.forename: Sandra
authors.initials: S
authors.lastname: Ortega-Martorell
authors.affiliation: Institute of Biotechnology, The University of Manchester, Manchester, UK. Ivan.Olier@manchester.ac.uk.
authors.forename: Iván
authors.initials: I
authors.lastname: Olier
authors.affiliation: Institute of Scientific Instruments of the CAS, v. v. i, Brno, Czech Republic. jmj@isibrno.cz.
authors.forename: Michal
authors.initials: M
authors.lastname: Jablonski
authors.affiliation: Institute of Scientific Instruments of the CAS, v. v. i, Brno, Czech Republic. jana@isibrno.cz.
authors.forename: Jana
authors.initials: J
authors.lastname: Starcukova
authors.affiliation: School of Computing and Mathematical Sciences, Liverpool John Moores University, Liverpool, UK. P.J.Lisboa@ljmu.ac.uk.
authors.forename: Paulo
authors.initials: P
authors.lastname: Lisboa
authors.affiliation: Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, UAB, Cerdanyola del Vallès, Barcelona, 08193, Spain. carles.arus@uab.es.|Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina CIBER-BBN, Cerdanyola del Vallès, Barcelona, Spain. carles.arus@uab.es.|Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain. carles.arus@uab.es.
authors.forename: Carles
authors.initials: C
authors.lastname: Arús
authors.affiliation: Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, UAB, Cerdanyola del Vallès, Barcelona, 08193, Spain. Margarita.Julia@uab.cat.|Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina CIBER-BBN, Cerdanyola del Vallès, Barcelona, Spain. Margarita.Julia@uab.cat.|Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain. Margarita.Julia@uab.cat.
authors.forename: Margarida
authors.initials: M
authors.lastname: Julià-Sapé
mesh_terms: D000465:Algorithms; D001330:Electronic Data Processing / Q000706:statistics & numerical data*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D012984:Software