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.

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

EPLVSD

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.

FiTAID

Chong DGQ, Kreis R, Bolliger CS, Boesch C, Slotboom J. Two-dimensional linear-combination model fitting of magnetic resonance spectra to define the macromolecule baseline using FiTAID, a fitting tool for arrays of interrelated datasets. MAGMA. 2011;24:147–164.

Adalid V, Döring A, Kyathanahally SP, Bolliger CS, Boesch C, Kreis R. Fitting interrelated datasets: metabolite diffusion and general lineshapes. MAGMA 2017;30(5):429-448.

For the RANDOM algorithm see: Slotboom J, Hofmann L, Boesch C, and Kreis R. Spectral fitting in a constrained parameter space using a random search strategy and prior knowledge. 6th Meeting of the International Society of Magnetic Resonance in Medicine, Sydney, 1998; p.26

Gabor

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

HLSVD

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.

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

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.

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

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

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.

LPSVD(CR)

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.

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).

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.

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