| Literature DB >> 26329486 |
Franciszek Binczyk, Rafal Tarnawski, Joanna Polanska.
Abstract
UNLABELLED: Nuclear Magnetic Resonance (NMR) spectroscopy is a popular medical diagnostic technique. NMR is also the favourite tool of chemists/biochemists to elucidate the molecular structure of small or big molecules; it is also a widely used tool in material science, in food science etc. In the case of medical diagnosis it allows for determining a metabolic composition of analysed tissue which may support the identification of tumour cells. Precession signal, that is a crucial part of MR phenomenon, contains distortions that must be filtered out before signal analysis. One of such distortions is phase error. Five popular algorithms: Automics, Shanon’s entropy minimization, Ernst’s method, Dispa and eDispa are presented and discussed. A novel adaptive tuning algorithm for Automics method was developed and numerically optimal solutions to automatic tuning of the other four algorithms were proposed. To validate the performance of the proposed techniques, two experiments were performed - the first one was done with the use of in silico generated data. For all presented methods, the fine tuning strategies significantly increased the correction accuracy. The highest improvement was observed for Automics algorithm, independently of noise level, with relative phase error dropping by average from 10.25% to 2.40% for low noise level and from 12.45% to 2.66% for high noise level. The second validation experiment, done with the use of phantom data, confirmed the in silico results. The obtained accuracy of the estimation of metabolite concentration was at 99.5%.Entities:
Mesh:
Year: 2015 PMID: 26329486 PMCID: PMC4648061 DOI: 10.1186/1475-925X-14-S2-S5
Source DB: PubMed Journal: Biomed Eng Online ISSN: 1475-925X Impact factor: 2.819
Figure 1a) Spectrum before phase correction, b) spectrum after correction with random initial condition, c) spectrum corrected with proposed initial condition.
Figure 2Visualization of idea behind assumed quality criterion [15].
Figure 3Exemplary spectrum obtained with the addition of the phase error equal to 10 degrees and low level noise. [15]
Figure 4Proposed experiment scheme. Both tuned and not tuned methods are examined [15].
Figure 7Distributions of metabolite concentration calculated for 27 spectra obtained on brain phantom. For each spectrum two experiments were performed: with phase correction by original Automics algorithm (original) and second by tuned Automics (tuned). Boxplots represent median and upper and lower quartiles of distribution, Tukey's criterion was used for outlier detection (marked as dots). For each metabolite desired value is indicated by dotted line.
Results of the analysis of 27 brain phantom spectra obtained for two different phase correction algorithms: original Automics and Automics with proposed tunning applied.
| Metabolite | not tuned | tuned | paired t-test p-values | ||||||
|---|---|---|---|---|---|---|---|---|---|
| s | 95% CI | CV [%] | s | 95% CI | CV [%] | ||||
| NAA | 12.32 | 0.87 | (12.25; 12.39) | 7.48 | 12.51 | 0.24 | (12.33; 12.69) | 2.33 | 0.0023 |
| Creatine | 9.51 | 0.79 | (9.45; 9.57) | 8.36 | 10.04 | 0.09 | (9.95; 10.13) | 1.15 | 0.0048 |
| Choline | 2.87 | 0.14 | (2.86; 2.88) | 4.93 | 3.00 | 0.06 | (2.85; 3.14) | 1.89 | 0.0023 |
| myo-Inositol | 6.67 | 0.73 | (6.61; 6.73) | 10.81 | 7.49 | 0.06 | (7.38; 7.59) | 1.36 | 0.0048 |
| Lactate | 4.72 | 0.58 | (4.67; 4.76) | 12.07 | 5.02 | 0.12 | (4.86; 5.17) | 2.00 | 0.0023 |
The presented descriptive statistics are: sample mean , sample standard deviation (s), 95% confidence interval for population mean value (95%CI) and coefficient of variation (CV). Right column presents paired t test p-value resulting from testing the hypothesis on no accuracy improvement by algorithm tuning.
The statistics of location (mean) and dispersion (standard deviation and coefficient of variation) for relative phase error [%] obtained for phase correction algorithms before the application of tuning procedures - low noise.
| Automics | Shanon's | Ernst | Dispa | eDispa | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CV [%] | CV [%] | CV [%] | CV [%] | CV [%] | |||||||||||
| 5.00 | 9.84 | 0.99 | 10.06 | 8.89 | 0.91 | 10.24 | 3.01 | 0.98 | 32.56 | 6.31 | 1.03 | 16.32 | 6.35 | 1.01 | 15.91 |
| 7.50 | 9.99 | 1.02 | 10.22 | 9.01 | 0.94 | 10.38 | 3.28 | 0.94 | 28.51 | 7.06 | 0.96 | 13.53 | 6.57 | 1.03 | 15.61 |
| 10.00 | 10.11 | 1.04 | 10.32 | 9.18 | 0.93 | 10.17 | 3.62 | 0.93 | 25.78 | 7.32 | 0.94 | 12.89 | 6.83 | 1.06 | 15.56 |
| 12.50 | 10.19 | 1.05 | 10.28 | 9.31 | 0.92 | 9.91 | 3.89 | 0.94 | 24.08 | 7.44 | 0.98 | 13.21 | 7.32 | 1.06 | 14.51 |
| 15.00 | 10.26 | 1.03 | 10.06 | 9.39 | 0.92 | 9.80 | 4.50 | 0.93 | 20.71 | 7.46 | 0.98 | 13.19 | 7.99 | 1.09 | 13.59 |
| 17.50 | 10.37 | 1.04 | 10.06 | 9.51 | 0.92 | 9.70 | 4.87 | 0.92 | 18.88 | 7.75 | 0.97 | 12.56 | 8.40 | 1.11 | 13.15 |
| 20.00 | 10.45 | 1.04 | 9.96 | 9.64 | 0.91 | 9.44 | 5.31 | 0.93 | 17.50 | 7.72 | 1,00 | 12.99 | 8.94 | 1.13 | 12.60 |
| 22.50 | 10.49 | 1.02 | 9.68 | 9.70 | 0.9 | 9.28 | 5.82 | 0.93 | 15.98 | 7.67 | 1.05 | 13.62 | 9.73 | 1.12 | 11.51 |
| 25.00 | 10.55 | 0.97 | 9.19 | 9.69 | 0.91 | 9.39 | 6.93 | 0.91 | 13.13 | 7.55 | 0.99 | 13.11 | 10.67 | 1.18 | 11.06 |
The statistics of location (mean) and dispersion (standard deviation and coefficient of variation) for relative phase error [%] obtained for phase correction algorithms with applied tuning - low noise.
| Automics | Shanon's | Ernst | Dispa | eDispa | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CV [%] | CV [%] | CV [%] | CV [%] | CV [%] | |||||||||||
| 5.00 | 2.01 | 0.61 | 30.35 | 1.89 | 0.53 | 28.04 | 2.03 | 0.58 | 28.57 | 2.38 | 1.06 | 44.54 | 2.15 | 1.05 | 48.84 |
| 7.50 | 2.12 | 0.63 | 29.79 | 1.98 | 0.55 | 27.85 | 2.21 | 0.60 | 26.92 | 2.47 | 0.97 | 39.27 | 2.29 | 1.01 | 44.10 |
| 10.00 | 2.28 | 0.58 | 25.58 | 2.09 | 0.57 | 27.48 | 2.35 | 0.56 | 23.97 | 2.56 | 1.01 | 39.50 | 2.36 | 1.03 | 43.58 |
| 12.50 | 2.38 | 0.55 | 22.92 | 2.20 | 0.58 | 26.20 | 2.42 | 0.55 | 22.57 | 2.65 | 1.08 | 40.74 | 2.46 | 1.03 | 41.62 |
| 15.00 | 2.43 | 0.54 | 22.14 | 2.31 | 0.56 | 24.35 | 2.45 | 0.55 | 22.57 | 2.70 | 1.07 | 39.70 | 2.53 | 1.04 | 40.98 |
| 17.50 | 2.54 | 0.52 | 20.51 | 2.41 | 0.57 | 23.63 | 2.55 | 0.55 | 21.37 | 2.78 | 1.08 | 38.67 | 2.62 | 1.03 | 39.37 |
| 20.00 | 2.64 | 0.48 | 18.06 | 2.53 | 0.57 | 22.53 | 2.60 | 0.52 | 20.10 | 2.85 | 1.14 | 39.95 | 2.69 | 1.05 | 39.21 |
| 22.50 | 2.66 | 0.47 | 17.70 | 2.64 | 0.55 | 20.64 | 2.59 | 0.54 | 20.66 | 2.92 | 1.17 | 39.97 | 2.78 | 1.05 | 37.66 |
| 25.00 | 2.64 | 0.51 | 19.32 | 2.76 | 0.51 | 18.48 | 2.57 | 0.58 | 22.57 | 2.92 | 1.05 | 35.96 | 2.79 | 1.08 | 38.71 |
The statistics of location (mean) and dispersion (standard deviation and coefficient of variation) for relative phase error [%] obtained for phase correction algorithms before the application of tuning procedures - high noise.
| Automics | Shanon's | Ernst | Dispa | eDispa | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CV [%] | CV [%] | CV [%] | CV [%] | CV [%] | |||||||||||
| 5.00 | 12.25 | 1.61 | 13.14 | 10.25 | 1.75 | 17.07 | 5.67 | 1.55 | 27.34 | 8.03 | 1.88 | 23.41 | 8.55 | 2.05 | 23.98 |
| 7.50 | 12.29 | 1.64 | 13.30 | 10.46 | 1.86 | 17.74 | 5.75 | 1.62 | 28.09 | 8.09 | 2.04 | 25.17 | 8.62 | 2.09 | 24.19 |
| 10.00 | 12.33 | 1.66 | 13.47 | 10.56 | 1.83 | 17.36 | 5.79 | 1.75 | 30.22 | 8.13 | 1.95 | 24.04 | 8.78 | 2.39 | 27.26 |
| 12.50 | 12.38 | 1.64 | 13.27 | 10.64 | 1.78 | 16.75 | 5.96 | 1.76 | 29.45 | 8.26 | 1.99 | 24.10 | 9.55 | 2.52 | 26.33 |
| 15.00 | 12.42 | 1.64 | 13.23 | 10.71 | 1.76 | 16.42 | 6.19 | 1.78 | 28.81 | 8.34 | 1.98 | 23.69 | 10.12 | 2.55 | 25.24 |
| 17.50 | 12.47 | 1.65 | 13.25 | 10.82 | 1.76 | 16.26 | 6.32 | 1.84 | 29.14 | 8.42 | 2.00 | 23.76 | 10.51 | 2.68 | 25.49 |
| 20.00 | 12.51 | 1.65 | 13.19 | 10.88 | 1.69 | 15.57 | 6.48 | 1.89 | 29.23 | 8.51 | 1.94 | 22.76 | 11.12 | 2.87 | 25.78 |
| 22.50 | 12.57 | 1.62 | 12.89 | 10.93 | 1.65 | 15.05 | 6.78 | 1.83 | 26.99 | 8.66 | 2.01 | 23.21 | 12.13 | 2.80 | 23.04 |
| 25.00 | 12.61 | 1.65 | 13.08 | 10.97 | 1.66 | 15.13 | 7.09 | 1.89 | 26.66 | 8.67 | 1.92 | 22.15 | 12.39 | 2.71 | 21.87 |
The statistics of location (mean) and dispersion (standard deviation and coefficient of variation) for relative phase error [%] obtained for phase correction algorithms with applied tuning - high noise.
| Automics | Shanon's | Ernst | Dispa | eDispa | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CV [%] | CV [%] | CV [%] | CV [%] | CV [%] | |||||||||||
| 5.00 | 2.58 | 0.65 | 25.19 | 2.79 | 0.93 | 33.33 | 2.78 | 0.86 | 30.94 | 3.08 | 0.99 | 32.14 | 2.94 | 1.24 | 42.18 |
| 7.50 | 2.60 | 0.64 | 24.62 | 2.86 | 1.01 | 35.20 | 2.80 | 0.89 | 31.61 | 3.11 | 1.12 | 36.07 | 2.97 | 1.10 | 37.10 |
| 10.00 | 2.63 | 0.68 | 25.89 | 2.86 | 0.97 | 33.80 | 2.87 | 0.92 | 31.90 | 3.12 | 1.14 | 36.43 | 3.02 | 1.17 | 38.63 |
| 12.50 | 2.65 | 0.68 | 25.59 | 2.88 | 0.97 | 33.54 | 2.90 | 0.93 | 31.92 | 3.14 | 1.13 | 36.07 | 3.08 | 1.18 | 38.46 |
| 15.00 | 2.66 | 0.68 | 25.68 | 2.89 | 0.94 | 32.57 | 2.93 | 0.95 | 32.49 | 3.15 | 1.11 | 35.35 | 3.13 | 1.22 | 38.83 |
| 17.50 | 2.69 | 0.69 | 25.79 | 2.92 | 0.95 | 32.39 | 2.97 | 0.98 | 32.86 | 3.16 | 1.14 | 36.13 | 3.18 | 1.21 | 38.05 |
| 20.00 | 2.71 | 0.71 | 26.35 | 2.92 | 0.90 | 30.86 | 3.02 | 1.00 | 33.04 | 3.17 | 1.11 | 34.87 | 3.24 | 1.29 | 39.88 |
| 22.50 | 2.72 | 0.69 | 25.37 | 2.94 | 0.91 | 30.78 | 3.02 | 1.01 | 33.33 | 3.19 | 1.08 | 33.75 | 3.30 | 1.29 | 39.09 |
| 25.00 | 2.73 | 0.71 | 26.01 | 2.95 | 0.85 | 28.81 | 3.06 | 1.06 | 34.64 | 3.17 | 1.03 | 32.49 | 3.36 | 1.35 | 40.18 |