Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance
Jazyk angličtina Země Anglie, Velká Británie Médium electronic
Typ dokumentu časopisecké články
PubMed
28114896
PubMed Central
PMC5260066
DOI
10.1186/s12859-017-1459-5
PII: 10.1186/s12859-017-1459-5
Knihovny.cz E-zdroje
- Klíčová slova
- Magnetic Resonance Spectroscopy, SQL database, Signal Processing, jMRUI,
- MeSH
- algoritmy MeSH
- automatizované zpracování dat * MeSH
- databáze faktografické MeSH
- magnetická rezonanční spektroskopie * MeSH
- magnetická rezonanční tomografie * MeSH
- reprodukovatelnost výsledků MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In order to obtain any metabolic information from measured spectra a processing should be done in specialized software, like jMRUI. The processing is interactive and complex and often requires many trials before obtaining a correct result. This paper proposes a jMRUI enhancement for efficient and unambiguous history tracking and file identification. RESULTS: A database storing all processing steps, parameters and files used in processing was developed for jMRUI. The solution was developed in Java, authors used a SQL database for robust storage of parameters and SHA-256 hash code for unambiguous file identification. The developed system was integrated directly in jMRUI and it will be publically available. A graphical user interface was implemented in order to make the user experience more comfortable. The database operation is invisible from the point of view of the common user, all tracking operations are performed in the background. CONCLUSIONS: The implemented jMRUI database is a tool that can significantly help the user to track the processing history performed on data in jMRUI. The created tool is oriented to be user-friendly, robust and easy to use. The database GUI allows the user to browse the whole processing history of a selected file and learn e.g. what processing lead to the results, where the original data are stored, to obtain the list of all processing actions performed on spectra.
Faculty of Science Masaryk University Kotlářská 267 2 611 37 Brno Czech Republic
Institute of Scientific Instruments of the CAS Královopolská 147 612 64 Brno Czech Republic
Zobrazit více v PubMed
Oz G, Alger JR, Barker PB, Bartha R, Bizzi A, Boesch C, et al. Clinical proton MR spectroscopy in central nervous system disorders. Radiology. 2014;270(3):658–79. doi: 10.1148/radiol.13130531. PubMed DOI PMC
Govindaraju V, Young K, Maudsley AA. Proton NMR chemical shifts and coupling constants for brain metabolites. NMR Biomed. 2000;13(3):129–53. doi: 10.1002/1099-1492(200005)13:3<129::AID-NBM619>3.0.CO;2-V. PubMed DOI
Bendahan D, Mattéi JP, Kozak-Ribbens G, Cozzone PJ. Non-invasive investigation of muscle diseases using 31P magnetic resonance spectroscopy: potential in clinical applications. Revue Neurologique. 2002;158(5 Pt 1):527–540. PubMed
Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R. Simultaneous in vivo spectral editing and water suppression. NMR Biomed. 1998;11:266–272. doi: 10.1002/(SICI)1099-1492(199810)11:6<266::AID-NBM530>3.0.CO;2-J. PubMed DOI
Bottomley PA. Spatial Localization in NMR Spectroscopy in Vivo. Annals of the New York Academy of Sciences. 1987;508:333–348. doi: 10.1111/j.1749-6632.1987.tb32915.x. PubMed DOI
Frahm J, Klaus-Dietmar Merboldt, Hänicke W. Localized proton spectroscopy using stimulated echoes. J Magn Reson. 1987;3:502–508.
Garwood M, DelaBarre L. The return of the frequency sweep: designing adiabatic pulses for contemporary NMR. J Magn Reson. 2001;2:155–177. doi: 10.1006/jmre.2001.2340. PubMed DOI
Scheenen TW, Klomp DW, Wijnen JP, Heerschap A. Short echo time 1H-MRSI of the human brain at 3 T with minimal chemical shift displacement errors using adiabatic refocusing pulses. Magn Reson Med. 2008;59(1):1–6. doi: 10.1002/mrm.21302. PubMed DOI
Mlynárik V, Gambarota G, Frenkel H, Gruetter R. Localized short-echo-time proton MR spectroscopy with full signal-intensity acquisition. Magn Reson Med. 2006;56(5):965–70. doi: 10.1002/mrm.21043. PubMed DOI
Kreis R. Issues of spectral quality in clinical 1H-magnetic resonance spectroscopy and a gallery of artifacts. NMR Biomed. 2004;17(6):361–81. doi: 10.1002/nbm.891. PubMed DOI
Stefan D, Di Cesare F, Andrasescu A, Popa E, Lazariev A, Vescovo E, Strbak O, Williams S, Starcuk Z, Cabanas M, van Ormondt D, Graveron-Demilly D. Quantitation of magnetic resonance spectroscopy signals: the jMRUI software package. Meas. Sci. Technol. 2009;20:104035.
Provencher SW. Estimation of metabolite concentrations from localized in vivo proton NMR spectra. Magn Reson Med. 1993;30(6):672–9. doi: 10.1002/mrm.1910300604. PubMed DOI
Wilson M, Reynolds G, Kauppinen RA, Arvanitis TN, Peet AC. A constrained least-squares approach to the automated quantitation of in vivo (1)H magnetic resonance spectroscopy data. Magn Reson Med. 2011;65(1):1–12. doi: 10.1002/mrm.22579. PubMed DOI
Graveron-Demilly D. Quantification in magnetic resonance spectroscopy based on semi-parametric approaches. MAGMA. 2014;27(2):113–30. doi: 10.1007/s10334-013-0393-4. PubMed DOI
Vanhamme L, van den Boogaart A, Van Huffel S. Improved method for accurate and efficient quantification of MRS data with use of prior knowledge. J Magn Reson. 1997;129:35–43. doi: 10.1006/jmre.1997.1244. PubMed DOI
Poullet JB, Sima DM, Simonetti AW, de Neuter B, Vanhamme L, Lemmerling P, Van Huffel S. An automated quantitation of short echo time MRS spectra in an open source software environment: AQSES. NMR Biomed. 2007;20(5):493–504. doi: 10.1002/nbm.1112. PubMed DOI
Ratiney H, Sdika M, Coenradie Y, Cavassila S, van Ormondt D, Graveron-Demilly D. Time-domain semi-parametric estimation based on a metabolite basis set. NMR Biomed. 2005;2005(18):1–13. doi: 10.1002/nbm.895. PubMed DOI
Pijnappel WWF, van den Boogaart A, de Beer R, van Ormondt D. SVD-based quantification of magnetic resonance signals. J Magn Reson. 1992;97:122–134.
Starcuk Z, Starcukova J, Strbak O, Graveron-Demilly D. Simulation of coupled-spin systems in the steady-state free precession acquisition mode for fast magnetic resonance (MR) spectroscopic imaging. Meas Sci Technol. 2009;20:104033. doi: 10.1088/0957-0233/20/10/104033. DOI
By: in ’t Zandt, H; van Der Graaf, M; Heerschap, A, Common processing of in vivo MR spectra. NMR in biomedicine doi: 10.1002/nbm.707 PubMed
H2 Database Engine http://www.h2database.com/html/main.html 15 July 2016
Mocioiu V, Ortega-Martorell S, Olier I, Jablonski M, Starcukova J, Lisboa P, Arús C, Julià-Sapé M. From raw data to data-analysis for magnetic resonance spectroscopy – the missing link: jMRUI2XML. BMC Bioinformatics. 2015 PubMed PMC