Scientific & technical literature

jMRUI references

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. Measurement Science and Technology 20:104035 (9 pp), 2009. doi: 10.1088/0957-0233/20/10/104035

Naressi, A., Couturier, C., Castang, I., de Beer, R. Graveron-Demilly, D. Java-based graphical user interface for MRUI, a software package for quantitation of in vivo/medical magnetic resonance spectroscopy signals. Computers in Biology and Medicine 31: 269-86, 2001.

Naressi, A., Couturier, C., Devos, J.M., Janssen, M., Mangeat, C., de Beer, R., Graveron-Demilly, D. Java-based graphical user interface for the MRUI quantitation package. MAGMA 12: 141-52, 2001. doi: 10.1007/BF02668096

van den Boogaart, A. (1997). MRUI MANUAL V. 96.3. A user’s guide to the Magnetic Resonance User Interface Software Package. Delft Technical University Press, Delft. ISBN: 90-9010509-3.

van den Boogaart, A., Van Hecke, P., Van Huffel, S., Graveron-Demilly, D., van Ormondt, D., de Beer, R. MRUI: a graphical user interface for accurate routine MRS data analysis. In: Proceedings of the ESMRMB 13th Annual Meeting, Prague, p. 318, 1996.

Algorithm references

AMARES – Vanhamme, L., van den Boogaart, A., Van Huffel, S. Improved method for accurate and efficient quantification of MRS data with use of prior knowledge. Journal of Magnetic Resonance 129: 35-43, 1997.

CADZOW Enhancement Procedure (EP) – Diop, A., Zaim-Wadghiri, Y., Briguet, A., Graveron-Demilly, D. Improvements of quantitation by using the Cadzow enhancement procedure prior to any linear-prediction methods. Journal of Magnetic Resonance B 105: 17-24, 1994.

CADZOW Enhancement Procedure (EP) – Diop, A., Briguet, A., Graveron-Demilly, D. Automatic in vivo NMR data processing based on an enhancement procedure and linear prediction method. Magnetic Resonance in Medicine 27: 318-328, 1992.

DATABASE HISTORY TRACKING – Jabłoński M., Starcukova J.,  Starcuk Z. Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance DOI: 10.1186/s12859-017-1459-5

EPLSVD – Diop, A., Kölbel, W., Michel, D., Briguet, A., Graveron-Demilly, D. Full automation of quantitation of in vivo NMR by LPSVD(CR) and EPLPSVD. Journal of Magnetic Resonance B 103: 217-221, 1994.

ER Filter – Cavassila, S., Fenet, B., van den Boogaart, A., Rémy, C., Briguet, C., Graveron-Demilly, D. ER-Filter: a preprocessing technique to improve the performance of SVD-based quantitation methods. Journal of Magnetic Resonance Analysis 3: 87-92, 1997.

GABOR – algorithm – Feichtinger, H.G., Strohmer, T., Gabor Analysis and Algorithms — Theory and Applications, Birkhäuser, 1998, Boston.

HLSVD – algorithm – Pijnappel, W.W.F., van den Boogaart, A., de Beer, R., van Ormondt, D. SVD-based quantification of magnetic resonance signals. Journal of Magnetic Resonance 97: 122-134, 1992.

HLSVD water filtering – van den Boogaart, A., van Ormondt, D., Pijnappel, W.W.F., de Beer, R., and Ala-Korpela, M. (1994). In Mathematics in Signal Processing III, (J.G. McWhirter, Ed.), pp. 175-195, Clarendon Press, Oxford.

HSVD – algorithm – Barkhuijsen, H, de Beer, R, van, Ormondt, D. Improved algorithm for noniterative time-domain model fitting to exponentially damped magnetic resonance signals. Journal of Magnetic Resonance 73: 553-557, 1987.

HSVD – algorithm – Barkhuijsen, H, de Beer, R, Bovée, W.M.M.J., van, Ormondt, D. Retrieval of frequencies, amplitudes, damping factors, and phases from time-domain signals using a linear least-squares procedure. Journal of Magnetic Resonance 61: 465-481, 1985.

HTLS – Algorithm – Van Huffel, S., Chen, H., Decanniere, C., Van Hecke, P. Algorithm for the time-domain NMR data fitting based on total least squares. Journal of Magnetic Resonance A 110: 228-237, 1994

HTLS – Application –  Chen, H., Van Huffel, S., Decanniere, C., Van Hecke, P. A signal-enhancement algorithm for the quantification of NMR data in the time domain. Journal of Magnetic Resonance A 109: 46-55, 1994.

jMRUI, MRUI for Java – Naressi, A., Couturier, C., Devos, J.M., Janssen, M., Mangeat, C., de Beer, R., Graveron-Demilly, D. Java-based graphical user interface for the MRUI quantitation package. MAGMA, 2001 (in press).

LPSVD(CR) – Algorithm – Kölbel, W., Schäfer, H. Improvement and automation of the LPSVD algorithm by continuous regularization of the singular values. Journal of Magnetic Resonance B 100: 598-603, 1992.

LPSVD(CR) – Application – Diop, A., Kölbel, W., Michel, D., Briguet, A., Graveron-Demilly, D. Full automation of quantitation of in vivo NMR by LPSVD(CR) and EPLPSVD. Journal of Magnetic Resonance B 103: 217-221, 1994.

NMRSCOPE-B – Z Starcuk Jr, J Starcukova, O Strbak and D Graveron-Demilly: Simulation of coupled-spin systems in the steady-state free-precession acquisition mode for fast magnetic resonance (MR) spectroscopic imaging. Meas. Sci. Technol. 20, 10, 104033 (2009).

NMRSCOPE-B  Z Starcuk Jr, J Starcukova; Quantum-mechanical simulations for in vivo MR spectroscopy: Principles and possibilities demonstrated with the program NMRScopeB. Anal Biochem. DOI: 10.1016/j.ab.2016.10.007.

QUALITY – de Graaf, A.A., van Dijk, J.E., Bovée, W.M.M.F. QUALITY: quantification improvement by converting to the Lorentzian type. Magnetic Resonance in Medicine 13: 343-357, 1990.

SPECTRIM – Pedrosa de Barros, Nuno, Richard McKinley, Urspeter Knecht, Roland Wiest, and Johannes Slotboom. “Automatic quality control in clinical 1H MRSI of brain cancer.” NMR in Biomedicine (2016).

VARPRO – van der Veen, J.W.C., de Beer, R., Luyten, P.R., van Ormondt, D. Accurate quantification of in vivo 31-P NMR signals using the variable projection method and prior knowledge. Magnetic Resonance in Medicine 6: 92-98, 1988.

VARPRO – Frequency selective – Knijn, A., de Beer, R., van Ormondt, D. Frequency-selective quantification in the time domain. Journal of Magnetic Resonance 97: 444-450, 1992.

WATER Deconvolution – Klose, U. In vivo proton spectroscopy in presence of eddy currents. Magnetic Resonance in Medicine 14: 26-30, 1990.

WATER Filtering – See HLSVD and HLSVD water filtering references.

 

 

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