All Publications

  • Reconstruction of undersampled 3D non-Cartesian image-based navigators for coronary MRA using an unrolled deep learning model. Magnetic resonance in medicine Malave, M. O., Baron, C. A., Koundinyan, S. P., Sandino, C. M., Ong, F., Cheng, J. Y., Nishimura, D. G. 2020


    PURPOSE: To rapidly reconstruct undersampled 3D non-Cartesian image-based navigators (iNAVs) using an unrolled deep learning (DL) model, enabling nonrigid motion correction in coronary magnetic resonance angiography (CMRA).METHODS: An end-to-end unrolled network is trained to reconstruct beat-to-beat 3D iNAVs acquired during a CMRA sequence. The unrolled model incorporates a nonuniform FFT operator in TensorFlow to perform the data-consistency operation, and the regularization term is learned by a convolutional neural network (CNN) based on the proximal gradient descent algorithm. The training set includes 6,000 3D iNAVs acquired from 7 different subjects and 11 scans using a variable-density (VD) cones trajectory. For testing, 3D iNAVs from 4 additional subjects are reconstructed using the unrolled model. To validate reconstruction accuracy, global and localized motion estimates from DL model-based 3D iNAVs are compared with those extracted from 3D iNAVs reconstructed with l 1 -ESPIRiT. Then, the high-resolution coronary MRA images motion corrected with autofocusing using the l 1 -ESPIRiT and DL model-based 3D iNAVs are assessed for differences.RESULTS: 3D iNAVs reconstructed using the DL model-based approach and conventional l 1 -ESPIRiT generate similar global and localized motion estimates and provide equivalent coronary image quality. Reconstruction with the unrolled network completes in a fraction of the time compared to CPU and GPU implementations of l 1 -ESPIRiT (20* and 3* speed increases, respectively).CONCLUSIONS: We have developed a deep neural network architecture to reconstruct undersampled 3D non-Cartesian VD cones iNAVs. Our approach decreases reconstruction time for 3D iNAVs, while preserving the accuracy of nonrigid motion information offered by them for correction.

    View details for DOI 10.1002/mrm.28177

    View details for PubMedID 32011021

  • Computational MRI With Physics-Based Constraints: Application to Multicontrast and Quantitative Imaging IEEE SIGNAL PROCESSING MAGAZINE Tamir, J. I., Ong, F., Anand, S., Karasan, E., Wang, K., Lustig, M. 2020; 37 (1): 94–104
  • General phase regularized reconstruction using phase cycling MAGNETIC RESONANCE IN MEDICINE Ong, F., Cheng, J. Y., Lustig, M. 2018; 80 (1): 112–25


    To develop a general phase regularized image reconstruction method, with applications to partial Fourier imaging, water-fat imaging and flow imaging.The problem of enforcing phase constraints in reconstruction was studied under a regularized inverse problem framework. A general phase regularized reconstruction algorithm was proposed to enable various joint reconstruction of partial Fourier imaging, water-fat imaging and flow imaging, along with parallel imaging (PI) and compressed sensing (CS). Since phase regularized reconstruction is inherently non-convex and sensitive to phase wraps in the initial solution, a reconstruction technique, named phase cycling, was proposed to render the overall algorithm invariant to phase wraps. The proposed method was applied to retrospectively under-sampled in vivo datasets and compared with state of the art reconstruction methods.Phase cycling reconstructions showed reduction of artifacts compared to reconstructions without phase cycling and achieved similar performances as state of the art results in partial Fourier, water-fat and divergence-free regularized flow reconstruction. Joint reconstruction of partial Fourier + water-fat imaging + PI + CS, and partial Fourier + divergence-free regularized flow imaging + PI + CS were demonstrated.The proposed phase cycling reconstruction provides an alternative way to perform phase regularized reconstruction, without the need to perform phase unwrapping. It is robust to the choice of initial solutions and encourages the joint reconstruction of phase imaging applications. Magn Reson Med 80:112-125, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

    View details for PubMedID 29159989

    View details for PubMedCentralID PMC5876131

  • Robust 4D Flow Denoising Using Divergence-Free Wavelet Transform MAGNETIC RESONANCE IN MEDICINE Ong, F., Uecker, M., Tariq, U., Hsiao, A., Alley, M. T., Vasanawala, S. S., Lustig, M. 2015; 73 (2): 828-842


    To investigate four-dimensional flow denoising using the divergence-free wavelet (DFW) transform and compare its performance with existing techniques.DFW is a vector-wavelet that provides a sparse representation of flow in a generally divergence-free field and can be used to enforce "soft" divergence-free conditions when discretization and partial voluming result in numerical nondivergence-free components. Efficient denoising is achieved by appropriate shrinkage of divergence-free wavelet and nondivergence-free coefficients. SureShrink and cycle spinning are investigated to further improve denoising performance.DFW denoising was compared with existing methods on simulated and phantom data and was shown to yield better noise reduction overall while being robust to segmentation errors. The processing was applied to in vivo data and was demonstrated to improve visualization while preserving quantifications of flow data.DFW denoising of four-dimensional flow data was shown to reduce noise levels in flow data both quantitatively and visually. Magn Reson Med 73:828-842, 2015. © 2014 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.25176

    View details for Web of Science ID 000348139500043

    View details for PubMedID 24549830

    View details for PubMedCentralID PMC4139475