Peak-specific phase correction for automated spectrum processing of in vivo magnetic resonance spectroscopic imaging by using the multiscale approach.

NIH Public Access Author Manuscript Bo Pu Xue Za Zhi. Author manuscript; available in PMC 2014 May 23.

NIH-PA Author Manuscript

Published in final edited form as: Bo Pu Xue Za Zhi. 2014 March 5; 31(1): 32–39.

Peak-specific phase correction for automated spectrum processing of in vivo magnetic resonance spectroscopic imaging by using the multiscale approach Xiaodong Zhang1,* and Xiaoping Hu2 1Yerkes

Imaging Center and Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA

2Biomedical

Imaging Technique Center, The Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA 30322, USA


Abstract Automatic metabolite quantification with curve fitting is essential in analyzing large amount of in vivo magnetic resonance spectroscopic imaging (MRSI) data. However, such data analysis is usually hindered by distorted metabolite peaks and baselines normally seen in in vivo MRS. In the present study, a multiscale approach was utilized for peak-specific automatic phase correction in multi-slice MRSI data of human brain. The results suggest that this novel approach can improve the robustness and efficiency of metabolite quantification and facilitate automatic analysis of multi-slice in vivo MRSI data in human brain.

Keywords MRSI; spectral curve fitting; multiscale analysis; in vivo MR spectroscopy; chemical shift imaging (CSI); automatic phase correction

Introduction NIH-PA Author Manuscript

In vivo proton magnetic resonance spectroscopic imaging (MRSI) or chemical shift imaging (CSI) is a non-invasive multi-voxel approach to detect the neurochemical distribution of the brain and has been widely used in preclinical and clinic studies 1–9. Comprehensive data processing strategies have been developed for robust metabolite mapping of the human brain 10. However, because of gradient induced eddy currents, local susceptibility variations and drift of the static field 11,12, water suppression and lipid and macromolecule signals, in vivo MRSI of the brain is often associated with poor line shape and phase and baseline distortion. Reference signal based deconvolution is sometimes used to correct the phase errors arising from various instrument imperfections in order to obtain pure absorption spectra for quantification. While the reference scan approach is applicable in many situations, it prolongs the experimental time, particularly for multi-slice or whole brain

*

Correspondence to: Dr. Xiaodong Zhang, 954 Gatewood Rd NE, Atlanta, GA 30329, USA, Telephone: 1-404-712-9874, Fax: 1-404-712-9917, [email protected].

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studies. Furthermore, deconvolution with single reference peak only accounts for a zeroorder phase error and is inadequate when high order phase corrections are needed. Many automated quantification approaches are developed for one-dimensional NMR spectra or single voxel MRS 13–17. In addition, LC-model is a robust in vivo MRS processing package which uses a basis set for automatic metabolite quantification with single voxel or multivoxel data analysis 18. However, the popularity and application are limited in general MRS/ MRSI users due to license cost.


Due to the complexity in quantifying cerebral metabolites with in vivo MRS, most approaches incorporate the use of prior knowledge in order to simplify the computational procedure and derive more reliable results. The prior knowledge can be obtained experimentally or empirically 13,19,20 to improves the spectral peak fitting for automatic quantification of brain metabolites. However, these approaches are not always robust and/or efficient when applied to multi-slice in vivo MRSI data because of large variations in the spectral line-shape, peak location, and baseline from voxel to voxel in different brain regions. As a result, the metabolite mapping can be biased by using a single piece of prior knowledge for fitting every spectrum in multi-slice MRSI. A multiscale approach for analyzing the in vivo MRSI has been explored previously21. In the multiscale approach, a pyramid representation of the original data is created by recursively averaging the voxels in each block from the bottom level to the top level. As a result, the spectra on the top of the pyramid have the best SNR (and poorest spatial resolution) due to voxel averages, while the ones at the bottom remain unchanged. The desired analysis is applied to the pyramid in a top-down fashion with the analysis at each scale guided by results at its previous scale as prior knowledge to define initial values of fitting parameters (such as peak frequency, linewidth) and boundary constrains to simplify the optimization procedure of the curve fitting. This procedure is repeated until the bottom of the tree (i.e., the full resolution) is reached. Therefore, the prior knowledge of each voxel is estimated from the voxel itself and its neighbors. The multiscale approach has been demonstrated to be robust in the automatic analysis of MRSI in the human brain21. However, the need for phase correction in preprocessing may complicate the data analysis procedure in multi-slice or whole brain MRSI data analysis. In the present work, we implemented a robust and simple method for automatic quantification in multi-slice in vivo MRSI by incorporating the peak-specific phase-correction in the multiscale strategy.


Methods and materials 1.1 Data acquisition Two-slice in vivo proton MRSI data sets were acquired with a circular k-space coverage of 36-point diameter in normal volunteers (with proper consent and institutional approval) on a 1.5T whole body Siemens scanner (Siemens Medical Systems, Iselin, NJ) with the standard Siemens quadrature head coil. The customer-built MRSI pulse sequence used an inversion recovery prepared spin echo sequence (TR/TE/TI: 2000/135/170ms, FOV = 240mm × 240mm, slice thickness = 10mm) with 3 CHESS pulses for water suppression. The data acquisition took approximately 40 minutes.

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The original data matrix in each slice was 36×36×1024. The data were zero-filling to 64×64×4096 during the preprocessing. Also, to simplify the whole data processing procedure, each spectrum was divided into the N-acetyl-aspartate (NAA) segment and the segment containing Choline (Cho) and Creatine (Cr). The phase correction and peak fitting of each segment were performed independently. In addition, in order to improve data processing efficiency, a brain mask was created to retain only voxels in the brain and eliminate the unwanted voxels in each slice for the processing. 1.2 Data Processing The flowchart for the MRSI data analysis is illustrated in Fig. 1. All the data processing scripts were coded in MATLAB 5.2 (Mathworks, Inc., Boston, MA). The specific steps in the flowchart are described below.


MRSI Reconstruction—The MRSI data of each slice were reconstructed in the spatial and temporal domains by using FFT after Zero-padding. A zero-padding factor of 2 was used in each dimension for the interpolation purpose. A Hanning window function was applied in the spatial reconstruction, and a Lorentzian window function (linewidth = 2.5 Hz in this study) was used in the time domain during the spectral reconstruction of MRSI. As Lorentzian function is the natural line shape of a single spin NMR signal, the Lorentzian window function applied in the time domain affects the linewidth of each metabolite peak in the frequency domain due to apodization effect. Therefore, the linewidth of Lorentzian window function is defined based upon the SNR of acquired MRSI data as application of Lorentzian window function with larger linewidth will improve the spectral SNR but reduce spectral resolution.


Metabolite Peak Identification and Subspectrum Extraction: A three-level multiscale approach was employed for searching the peak locations, starting from the largest scale (i.e. poorest spatial resolution) and moving to the finest scale (i.e. highest spatial resolution). In the specific case of the present study, the first (bottom) level was composed of the original 64×64 data matrix. The second level was a 32 × 32 data matrix reconstructed by averaging each block of 2×2 voxels in the first level. Similarly, the third (top) level was a 16 × 16 data matrix reconstructed by averaging each block of 2×2 voxels in the second level. The multiscale approach permits the frequency and linewidth of each metabolite peak at one scale as prior knowledge for identifying the same metabolite peak at the next (finer) scale. During the coarse-to-fine optimization procedure of spectral peak identification, the NAA peak is located first at each level since it usually has the best signal-to-noise ratio (SNR). As the frequency difference between the NAA, and Cho or Cr peaks are fixed and known, the positions of Cho or Cr peak can be derived automatically after the NAA peak is identified. In the present study, the NAA segment and the segment containing Cho and Cr peaks were extracted from the original spectrum to simply the spectral fitting and reduce the calculation time in multi-slice MRSI (Fig. 2). Phase Correction—The phase correction was performed separately for each spectral segment. Although each spectrum is simplified due to the segmentation, its distorted baseline and phase varies from voxel to voxel, and not perfect in comparison with a standard


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absorption spectrum. Therefore, the contribution from both the real and imaginary parts is considered during the iterative optimization for automatic phase correction. The following function is minimized in the phase correction processing:

where W is an adjustable weighting factor to balance the contributions from the real and imaginary parts. W is adjusted empirically and its default value is estimated by equalizing contributions from the real (absorption) and imaginary (dispersion) parts which need to be maximized and minimized respectively. Subsequently, the real part of the spectrum was used for the spectral curve fitting in the next step. Metabolite Map Generation—A Gaussian line shape with a linear baseline was fitted to each peak with the least-square fitting. The area under the Gaussian peak was then calculated to give the metabolite level of the corresponding metabolite in each segmented spectrum.


Results and Discussion The stacked spectra of a set of healthy human brain MRSI data with and without the multiscale-based phase correction are displayed in Fig. 2. In comparison with the original spectra, the corrected spectra demonstrate well improved line shapes in either the NAA sections or Cho and Cr sections (Fig. 2b). The derived NAA, Cho, Cr metabolite maps for two-slice MRSI data set of the human brain are illustrated in Fig. 3.


As seen in the multiscale approach reported in the present study, the multiscale method is used to identify and localize the peaks of interest in each spectral segment and the peaks are then locally phase-corrected using an automatic algorithm proposed in the present study. Subsequently, the absorption spectra within these segments are curve-fitted to generate the corresponding metabolite map. By focusing on the metabolites of interest, each metabolite peak of interest can be isolated from the complex in vivo spectra containing signals from residual water, macromolecules, lipids, and other metabolites of no interest. Therefore, the phase correction procedure for each isolated peak is simplified substantially. Also, as the reconstructed spectra at the coarsest scale have best SNR, the peak identification (frequency and linewidth parameters) can be estimated automatically at the coarsest scale and the resultant peak information can be passed onto the next level as prior knowledge, making the procedure fully automatic. Although only the most widely examined metabolites, NAA, Cho, and Cr, were quantified in the present work, our approach can be applied to quantification of other metabolites. Also, as the prior information is used for locating the peaks of interest, it may be applicable in EPI-related MRSI data acquisition22,23 which has the reduced SNR or in large scale data processing for whole brain MRSI 8. Prior knowledge has been used in several studies of in vivo MRS data analysis 18–20, demonstrating their effectiveness in in vivo metabolite quantification. In general, the prior information in these studies is normally fixed and will not change from voxel to voxel to incorporate the large variation in peak position, line shape, baseline of every voxel in human


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brain in vivo MRSI. In addition, most previous approaches focus on the distorted baseline removal with complicated algorithms. In contrast, the multiscale approach provides the prior information of metabolite peaks from the averaged spectra on the top level of the pyramid, and then optimized progressively from the coarse spatial resolution to the fine one. Therefore, the prior knowledge for the spectral fitting of each voxel is self-adaptive and more reliable. In comparison with other reported approaches of in vivo MRSI data analysis, the multiscale-derived metabolite maps are comparable but the calculation procedure is much more simplified and robust and can be incorporated readily for various needs of spectral peak identification and spectrum curve fitting of in vivo MRSI.

Conclusion In summary, a robust algorithm has been presented for automatic metabolite quantifications of multi-slice in vivo proton MRSI. Results on in vivo MRSI data have demonstrated the effectiveness and robustness in metabolite quantification of human brain MRSI studies. The approach may be used for data processing of multi-slice in vivo MRSI in preclinical and clinical studies.


Acknowledgments This project was supported in part by the National Center for Research Resources (P51RR000165) of NIH and by the Office of Research Infrastructure Programs (OD P51OD011132).

References


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Fig. 1.

Flowchart of the data processing for multi-slice in vivo proton magnetic resonance spectroscopic imaging (MRSI) by using the multiscale approach


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NIH-PA Author Manuscript Fig. 2.

a) Uncorrected spectra from the in vivo proton MRSI data of a healthy human brain. b) Spectra with the phase distortion corrected by using the multiscale approach in the same MRSI data set.

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NIH-PA Author Manuscript Fig. 3.


T2-weighted images and cerebral metabolite maps are generated from the two-slice in vivo proton MRSI data of a healthy human brain with the phases corrected automatically by using the multiscale approach.


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