Nan-kuei Chen

Nan-kuei Chen

Associate Professor, Biomedical Engineering
Associate Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-0060

Research Interest

I am an MR physicist with extensive expertise in fast image acquisition methodology, pulse sequence design, and artifact correction for neuro MRI. In the past 18 years, I have developed novel approaches effectively addressing various types of challenging MRI artifacts, ranging from echo-planar imaging (EPI) geometric distortions, to susceptibility effect induced signal loss, to EPI Nyquist artifact, to motion-induced phase errors and aliasing artifacts in interleaved EPI based diffusion-weighted imaging. I am the original developer of multiplexed sensitivity encoded (MUSE) MRI, which can measure human brain connectivity in vivo at high spatial-resolution and accuracy, as shown in the publications listed below. More generally, my research involves the application of MR protocols in translational contexts. I have served as PI on NIH-funded R01, R21 and R03 grants, and have had extensive experience as a co-investigator on NIH-funded projects. The current focus of my research includes: * Development of high-throughput and motion-immune clinical MRI for imaging challenging patient populations * Imaging of neuronal connectivity networks for studies of neurological diseases * High-fidelity and multi-contrast MRI guided intervention * Characterization and correction of MRI artifacts * Signal processing and algorithm development * MRI studies of human development

Publications

Chu, M., Chang, H., Chung, H., Truong, T., Bashir, M. R., & Chen, N. (2015). POCS-based reconstruction of multiplexed sensitivity encoded MRI (POCSMUSE): A general algorithm for reducing motion-related artifacts. Magnetic resonance in medicine, 74(5), 1336-48.

A projection onto convex sets reconstruction of multiplexed sensitivity encoded MRI (POCSMUSE) is developed to reduce motion-related artifacts, including respiration artifacts in abdominal imaging and aliasing artifacts in interleaved diffusion-weighted imaging.

Song, X., Panych, L. P., & Chen, N. (2016). Data-Driven and Predefined ROI-Based Quantification of Long-Term Resting-State fMRI Reproducibility. Brain connectivity, 6(2), 136-51.

Resting-state functional magnetic resonance imaging (fMRI) is a promising tool for neuroscience and clinical studies. However, there exist significant variations in strength and spatial extent of resting-state functional connectivity over repeated sessions in a single or multiple subjects with identical experimental conditions. Reproducibility studies have been conducted for resting-state fMRI where the reproducibility was usually evaluated in predefined regions-of-interest (ROIs). It was possible that reproducibility measures strongly depended on the ROI definition. In this work, this issue was investigated by comparing data-driven and predefined ROI-based quantification of reproducibility. In the data-driven analysis, the reproducibility was quantified using functionally connected voxels detected by a support vector machine (SVM)-based technique. In the predefined ROI-based analysis, all voxels in the predefined ROIs were included when estimating the reproducibility. Experimental results show that (1) a moderate to substantial within-subject reproducibility and a reasonable between-subject reproducibility can be obtained using functionally connected voxels identified by the SVM-based technique; (2) in the predefined ROI-based analysis, an increase in ROI size does not always result in higher reproducibility measures; (3) ROI pairs with high connectivity strength have a higher chance to exhibit high reproducibility; (4) ROI pairs with high reproducibility do not necessarily have high connectivity strength; (5) the reproducibility measured from the identified functionally connected voxels is generally higher than that measured from all voxels in predefined ROIs with typical sizes. The findings (2) and (5) suggest that conventional ROI-based analyses would underestimate the resting-state fMRI reproducibility.

Truong, T., Chen, N., & Song, A. W. (2010). Application of k-space energy spectrum analysis for inherent and dynamic B0 mapping and deblurring in spiral imaging. Magnetic resonance in medicine, 64(4), 1121-7.

Spiral imaging is vulnerable to spatial and temporal variations of the amplitude of the static magnetic field (B(0)) caused by susceptibility effects, eddy currents, chemical shifts, subject motion, physiological noise, and system instabilities, resulting in image blurring. Here, a novel off-resonance correction method is proposed to address these issues. A k-space energy spectrum analysis algorithm is first applied to inherently and dynamically generate a B(0) map from the k-space data at each time point, without requiring any additional data acquisition, pulse sequence modification, or phase unwrapping. A simulated phase evolution rewinding algorithm and an automatic residual deblurring algorithm are then used to correct for the blurring caused by both spatial and temporal B(0) variations, resulting in a high spatial and temporal fidelity. This method is validated against conventional B(0) mapping and deblurring methods, and its advantages for dynamic MRI applications are demonstrated in functional MRI studies.

Lin, J., Tsai, S., Liu, H., Chung, H., Mulkern, R. V., Cheng, C., Yeh, T., & Chen, N. (2009). Quantification of non-water-suppressed MR spectra with correction for motion-induced signal reduction. Magnetic resonance in medicine, 62(6), 1394-403.

Intrascan subject movement in clinical MR spectroscopic examinations may result in inconsistent water suppression that distorts the metabolite signals, frame-to-frame variations in spectral phase and frequency, and consequent reductions in the signal-to-noise ratio due to destructive averaging. Frame-to-frame phase/frequency corrections, although reported to be successful in achieving constructive averaging, rely on consistent water suppression, which may be difficult in the presence of intrascan motion. In this study, motion correction using non-water-suppressed data acquisition is proposed to overcome the above difficulties. The time-domain matrix-pencil postprocessing method was used to extract water signals from the non-water-suppressed spectroscopic data, followed by phase and frequency corrections of the metabolite signals based on information obtained from the water signals. From in vivo experiments on seven healthy subjects at 3.0 T, quantification of metabolites using the unsuppressed water signal as a reference showed improved correlation with water-suppressed data acquired in the absence of motion (R(2) = 0.9669; slope = 0.94). The metabolite concentrations derived using the proposed approach were in good agreement with literature values. Computer simulations under various degrees of frequency and phase variations further demonstrated robust performance of the time-domain postprocessing approach.

Chen, N., & Wyrwicz, A. M. (2004). Removal of EPI Nyquist ghost artifacts with two-dimensional phase correction. Magnetic resonance in medicine, 51(6), 1247-53.

Odd-even echo inconsistencies result in Nyquist ghost artifacts in the reconstructed EPI images. The ghost artifacts reduce the image signal-to-noise ratio and make it difficult to correctly interpret the EPI data. In this article a new 2D phase mapping protocol and a postprocessing algorithm are presented for an effective Nyquist ghost artifacts removal. After an appropriate k-space data regrouping, a 2D map accurately encoding low- and high-order phase errors is derived from two phase-encoded reference scans, which were originally proposed by Hu and Le (Magn Reson Med 36:166-171;1996) for their 1D nonlinear correction method. The measured phase map can be used in the postprocessing algorithm developed to remove ghost artifacts in subsequent EPI experiments. Experimental results from phantom, animal, and human studies suggest that the new technique is more effective than previously reported methods and has a better tolerance to signal intensity differences between reference and actual EPI scans. The proposed method may potentially be applied to repeated EPI measurements without subject movements, such as functional MRI and diffusion coefficient mapping.