ProFit revisited

Magnetic Resonance in Medicine

Volumn 71, Issue 2, 2014, Pages 458-468

  Fuchs, Alexander ^a   Boesiger, Peter ^a   Schulte, Rolf F ^b   Henning, Anke ^a  

^a ETH ZURICH   (Switzerland)

^b GE GLOBAL RESEARCH   (Germany)

Author keywords

2D J resolved spectroscopy; 2D JPRESS; 2D macromolecular baseline; prior knowledge model fitting; ProFit; self deconvolution; spectral fitting

Indexed keywords

MACROMOLECULES; METABOLITES; SOFTWARE TESTING; SPECTROSCOPIC ANALYSIS;

2D JPRESS; 2D MACROMOLECULAR BASELINE; J-RESOLVED SPECTROSCOPY; PRIOR KNOWLEDGE; SELF-DECONVOLUTION; SPECTRAL FITTING;

PROFITABILITY;

ARTICLE; COMPUTER SIMULATION; HUMAN; HUMAN EXPERIMENT; IMAGE QUALITY; IMAGING SOFTWARE; IN VIVO STUDY; J RESOLVED SPECTROSCOPY; MATHEMATICAL MODEL; METABOLITE; NORMAL HUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; QUANTITATIVE ANALYSIS; RELIABILITY; BRAIN CHEMISTRY; COMPUTER PROGRAM; PROCEDURES; THEORETICAL MODEL;

BRAIN CHEMISTRY; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, THEORETICAL; SOFTWARE; SOFTWARE VALIDATION;

EID: 84892443428     PISSN: 07403194     EISSN: 15222594     Source Type: Journal    
DOI: 10.1002/mrm.24703     Document Type: Article

References (49)

1. Brandão L, Domingues R,. MR Spectroscopy of the brain. Philadelphia: Lippincott Williams & Wilkins; 2003.
2. 1H NMR spectroscopy of the human brain at high magnetic fields: metabolite quantification at 4T vs. 7T. Magn Reson Med 2009; 62: 868-879.
3. Luscher B, Shen Q, Sahir N,. The GABAergic deficit hypothesis of major depressive disorder. Mol Psychiatry 2010; 16: 383-406.
4. Yüksel C, Öngür D,. Magnetic resonance spectroscopy studies of glutamate-related abnormalities in mood disorders. Biol Psychiatry 2010; 68: 785-794.
5. Sanacora G, Zarate C, Krystal J, Manji H. Targeting the glutamatergic system to develop novel, improved therapeutics for mood disorders. Nat Rev Drug Discov 2008; 7: 426-437.
6. Thomas M, Yue K, Binesh N, et al. Localized two-dimensional shift correlated MR spectroscopy of human brain. Magn Reson Med 2001; 46: 58-67.
7. Andronesi O, Ramadan S, Mountford C, Sorensen A. Low-power adiabatic sequences for in vivo localized two-dimensional chemical shift correlated MR spectroscopy. Magn Reson Med 2010; 64: 1542-1556.
8. Lange T, Trabesinger A, Schulte R, Dydak U, Boesiger P. Prostate spectroscopy at 3 Tesla using two-dimensional S-PRESS. Magn Reson Med 2006; 56: 1220-1228.
9. Schulte R, Lange T, Beck J, Meier D, Boesiger P. Improved two-dimensional J-resolved spectroscopy. NMR Biomed 2006; 19: 264-270.
10. Naressi A, Couturier C, Devos J, Janssen M, Mangeat C, Beer Rd, Graveron-Demilly D. Java-based graphical user interface for the MRUI quantitation package. MAGMA 2001; 12: 141-152.
11. 1H short echo-time signals: background accommodation. MAGMA 2004; 16: 284-296.
12. 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; 18: 1-13.
13. Vanhamme L, van den Boogaart A, Van Huffel S,. Improved method for accurate and efficient quantification of MRS data with the use of prior knowledge. J Magn Reson 1997; 129: 35-43.
14. Reynolds G, Wilson M, Peet A, Arvanitis T. An algorithm for the automated quantitation of metabolites in in vitro NMR signals. Magn Reson Med 2006; 56: 1211-1219.
15. 1H magnetic resonance spectroscopy data. Magn Reson Med 2011; 65: 1-12.
16. Poullet J, Sima D, Simonetti A, 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: 493-504.
17. Provencher SW,. Estimation of metabolite concentrations from localized in vivo proton NMR spectra. Magn Reson Med 1993; 30: 672-679.
18. De Beer R, Van Ormondt D, Pijnappel W,. Quantification of 1-D and 2-D magnetic resonance time domain signals. Pure Appl Chem 1992; 64: 815-823.
19. Slotboom J, Boesch C, Kreis R,. Versatile frequency domain fitting using time domain models and prior knowledge. Magn Reson Med 1998; 39: 899-911.
20. Chong D, Kreis R, Bolliger C, 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. Magn Reson Mater Phys 2011; 1-18.
21. Jensen J, Licata S, Öngür D, Friedman S, Prescot A, Henry M, Renshaw P. Quantification of J-resolved proton spectra in two-dimensions with LCModel using GAMMA-simulated basis sets at 4 Tesla. NMR Biomed 2009; 22: 762-769.
22. Schulte R, Boesiger P,. ProFit: two-dimensional prior-knowledge fitting of J-resolved spectra. NMR Biomed 2006; 19: 255-263.
23. Maudsley A,. Spectral lineshape determination by self-deconvolution. J Magn Reson B 1995; 106: 47-57.
24. Sima D, Garcia M, Poullet J, Suvichakorn A, Antoine J, Van Huffel S, Van Ormondt D. Lineshape estimation for magnetic resonance spectroscopy (MRS) signals: self-deconvolution revisited. Meas Sci Technol 2009; 20: 104031.
25. Osorio-Garcia M, Sima D, Nielsen F, Himmelreich U, Van Huffel S. Quantification of magnetic resonance spectroscopy signals with lineshape estimation. J Chemometr 2011; 25: 183-192.
26. Golub G, Pereyra V,. The differentiation of pseudo-inverses and nonlinear least squares problems whose variables separate. SIAM J Numer Anal 1973; 10: 413-432.
27. 31P NMR signals using the variable projection method and prior knowledge. Magn Reson Med 1988; 6: 92-98.
28. Klose U,. In vivo proton spectroscopy in presence of Eddy currents. Magn Reson Med 1990; 14: 26-30.
29. 1H NMR spectra of human brain. Magn Reson Med 1994; 32: 294-302.
30. 2 relaxation in rat brain in vivo. Magn Reson Med 2006; 56: 386-394.
31. Starčuk Z, Starčuk Z Jr, Jaroslav H,. "Baseline" problems in very short echo-time proton MR spectroscopy of low molecular weight metabolites in the brain. Meas Sci Rev 2001; 1: 17-20.
32. Eilers P, Marx B,. Flexible smoothing with B-splines and penalties. Stat Sci 1996; 89-102.
33. Eilers P, Marx B,. Splines, knots, and penalties. Wiley Interdiscip Rev Comput Stat 2010; 2: 637-653.
34. De Graaf A, Van Dijk J, Bovée W,. QUALITY: quantification improvement by converting lineshapes to the Lorentzian type. Magn Reson Med 1990; 13: 343-357.
35. Bartha R, Drost D, Menon R, Williamson P. Spectroscopic lineshape correction by QUECC: combined QUALITY deconvolution and eddy current correction. Magn Reson Med 2000; 44: 641-645.
36. Metz K, Lam M, Webb A,. Reference deconvolution: a simple and effective method for resolution enhancement in nuclear magnetic resonance spectroscopy. Concepts Magn Reson 2000; 12: 21-42.
37. Boyd S, Vandenberghe L,. Convex optimization. Cambridge: Cambridge University Press; 2004.
38. Smith S, Levante T, Meier BH, Ernst R. Computer simulations in magnetic resonance. An object-oriented programming approach. J Magn Reson 1994;Series A 106: 75-105.
39. 2 relaxation times of human brain metabolites at 3 Tesla. NMR Biomed 2001; 14: 325-331.
40. 2 relaxation time of J-coupled cerebral metabolites in rat brain at 9.4T. NMR Biomed 2008; 21: 396-401.
41. 2 relaxation times and concentrations of cerebral metabolites. NMR Biomed 2012; 25: 332-339.
42. Govindaraju V, Young K, Maudsley AA,. Proton NMR chemical shifts and coupling constants for brain metabolites. NMR Biomed 2000; 13: 129-153.
43. 1H NMR spectroscopy at 7T. NMR Biomed 2010; 23: 227-232.
44. 1H NMR spectroscopy of rat brain at 1 ms echo time. Magn Reson Med 1999; 41: 649-656.
45. Schulte RF, Henning A, Tsao J, Boesiger P, Pruessmann KP. Design of broadband RF pulses with polynomial-phase response. J Magn Reson 2007; 186: 167-175.
46. Edden R, Barker P,. If J doesn't evolve, it won't J-resolve: J-PRESS with bandwidth-limited refocusing pulses. Magn Reson Med 2011; 65: 1509-1514.
47. Kaiser L, Young K, Meyerhoff D, Mueller S, Matson G. A detailed analysis of localized J-difference GABA editing: theoretical and experimental study at 4T. NMR Biomed 2008; 21: 22-32.
48. Sima D, Van Huffel S,. Regularized semiparametric model identification with application to nuclear magnetic resonance signal quantification with unknown macromolecular base-line. J R Statist Soc B 2006; 68: 383-409.
49. De Graaf R,. In vivo NMR spectroscopy: principles and techniques, 2nd ed. Chichester, UK: Wiley-Interscience; 2007.