Stanford Advisors

All Publications

  • Polynomial Preconditioners for Regularized Linear Inverse Problems. SIAM Journal on Imaging Sciences Iyer, S. S., Ong, F., Cao, X., Liao, C., Daniel, L., Tamir, J. I., Setsompop, K. 2024; 17:1 : 116-146

    View details for DOI 10.1137/22M1530355

  • DTI-MR fingerprinting for rapid high-resolution whole-brain T1 , T2 , proton density, ADC, and fractional anisotropy mapping. Magnetic resonance in medicine Cao, X., Liao, C., Zhou, Z., Zhong, Z., Li, Z., Dai, E., Iyer, S. S., Hannum, A. J., Yurt, M., Schauman, S., Chen, Q., Wang, N., Wei, J., Yan, Y., He, H., Skare, S., Zhong, J., Kerr, A., Setsompop, K. 2023


    This study aims to develop a high-efficiency and high-resolution 3D imaging approach for simultaneous mapping of multiple key tissue parameters for routine brain imaging, including T1 , T2 , proton density (PD), ADC, and fractional anisotropy (FA). The proposed method is intended for pushing routine clinical brain imaging from weighted imaging to quantitative imaging and can also be particularly useful for diffusion-relaxometry studies, which typically suffer from lengthy acquisition time.To address challenges associated with diffusion weighting, such as shot-to-shot phase variation and low SNR, we integrated several innovative data acquisition and reconstruction techniques. Specifically, we used M1-compensated diffusion gradients, cardiac gating, and navigators to mitigate phase variations caused by cardiac motion. We also introduced a data-driven pre-pulse gradient to cancel out eddy currents induced by diffusion gradients. Additionally, to enhance image quality within a limited acquisition time, we proposed a data-sharing joint reconstruction approach coupled with a corresponding sequence design.The phantom and in vivo studies indicated that the T1 and T2 values measured by the proposed method are consistent with a conventional MR fingerprinting sequence and the diffusion results (including diffusivity, ADC, and FA) are consistent with the spin-echo EPI DWI sequence.The proposed method can achieve whole-brain T1 , T2 , diffusivity, ADC, and FA maps at 1-mm isotropic resolution within 10 min, providing a powerful tool for investigating the microstructural properties of brain tissue, with potential applications in clinical and research settings.

    View details for DOI 10.1002/mrm.29916

    View details for PubMedID 37936313

  • High-fidelity mesoscale in-vivo diffusion MRI through gSlider-BUDA and circular EPI with S-LORAKS reconstruction. NeuroImage Liao, C., Yarach, U., Cao, X., Iyer, S. S., Wang, N., Kim, T. H., Tian, Q., Bilgic, B., Kerr, A. B., Setsompop, K. 2023: 120168


    To develop a high-fidelity diffusion MRI acquisition and reconstruction framework with reduced echo-train-length for less T2* image blurring compared to typical highly accelerated echo-planar imaging (EPI) acquisitions at sub-millimeter isotropic resolution.We first proposed a circular-EPI trajectory with partial Fourier sampling on both the readout and phase-encoding directions to minimize the echo-train-length and echo time. We then utilized this trajectory in an interleaved two-shot EPI acquisition with reversed phase-encoding polarity, to aid in the correction of off-resonance-induced image distortions and provide complementary k-space coverage in the missing partial Fourier regions. Using model-based reconstruction with structured low-rank constraint and smooth phase prior, we corrected the shot-to-shot phase variations across the two shots and recover the missing k-space data. Finally, we combined the proposed acquisition/reconstruction framework with an SNR-efficient RF-encoded simultaneous multi-slab technique, termed gSlider, to achieve high-fidelity 720μm and 500μm isotropic resolution in-vivo diffusion MRI.Both simulation and in-vivo results demonstrate the effectiveness of the proposed acquisition and reconstruction framework to provide distortion-corrected diffusion imaging at the mesoscale with markedly reduced T2*-blurring. The in-vivo results of 720μm and 500μm datasets show high-fidelity diffusion images with reduced image blurring and echo time using the proposed approaches.The proposed method provides high-quality distortion-corrected diffusion-weighted images with ∼40% reduction in the echo-train-length and T2* blurring at 500μm-isotropic-resolution compared to standard multi-shot EPI.

    View details for DOI 10.1016/j.neuroimage.2023.120168

    View details for PubMedID 37187364

  • Deep Learning Initialized Compressed Sensing (Deli-CS) in Volumetric Spatio-Temporal Subspace Reconstruction. bioRxiv : the preprint server for biology Iyer, S. S., Schauman, S. S., Sandino, C. M., Yurt, M., Cao, X., Liao, C., Ruengchaijatuporn, N., Chatnuntawech, I., Tong, E., Setsompop, K. 2023


    Introduction: Spatio-temporal MRI methods enable whole-brain multi-parametric mapping at ultra-fast acquisition times through efficient k-space encoding, but can have very long reconstruction times, which limit their integration into clinical practice. Deep learning (DL) is a promising approach to accelerate reconstruction, but can be computationally intensive to train and deploy due to the large dimensionality of spatio-temporal MRI. DL methods also need large training data sets and can produce results that don't match the acquired data if data consistency is not enforced. The aim of this project is to reduce reconstruction time using DL whilst simultaneously limiting the risk of deep learning induced hallucinations, all with modest hardware requirements.Methods: Deep Learning Initialized Compressed Sensing (Deli-CS) is proposed to reduce the reconstruction time of iterative reconstructions by "kick-starting" the iterative reconstruction with a DL generated starting point. The proposed framework is applied to volumetric multi-axis spiral projection MRF that achieves whole-brain T1 and T2 mapping at 1-mm isotropic resolution for a 2-minute acquisition. First, the traditional reconstruction is optimized from over two hours to less than 40 minutes while using more than 90% less RAM and only 4.7 GB GPU memory, by using a memory-efficient GPU implementation. The Deli-CS framework is then implemented and evaluated against the above reconstruction.Results: Deli-CS achieves comparable reconstruction quality with 50% fewer iterations bringing the full reconstruction time to 20 minutes.Conclusion: Deli-CS reduces the reconstruction time of subspace reconstruction of volumetric spatio-temporal acquisitions by providing a warm start to the iterative reconstruction algorithm.

    View details for DOI 10.1101/2023.03.28.534431

    View details for PubMedID 37034586

  • 3D-EPI blip-up/down acquisition (BUDA) with CAIPI and joint Hankel structured low-rank reconstruction for rapid distortion-free high-resolution T 2 * mapping. Magnetic resonance in medicine Chen, Z., Liao, C., Cao, X., Poser, B. A., Xu, Z., Lo, W. C., Wen, M., Cho, J., Tian, Q., Wang, Y., Feng, Y., Xia, L., Chen, W., Liu, F., Bilgic, B. 2023


    This work aims to develop a novel distortion-free 3D-EPI acquisition and image reconstruction technique for fast and robust, high-resolution, whole-brain imaging as well as quantitative T 2 * $$ {\mathrm{T}}_2^{\ast } $$ mapping.3D Blip-up and -down acquisition (3D-BUDA) sequence is designed for both single- and multi-echo 3D gradient recalled echo (GRE)-EPI imaging using multiple shots with blip-up and -down readouts to encode B0 field map information. Complementary k-space coverage is achieved using controlled aliasing in parallel imaging (CAIPI) sampling across the shots. For image reconstruction, an iterative hard-thresholding algorithm is employed to minimize the cost function that combines field map information informed parallel imaging with the structured low-rank constraint for multi-shot 3D-BUDA data. Extending 3D-BUDA to multi-echo imaging permits T 2 * $$ {\mathrm{T}}_2^{\ast } $$ mapping. For this, we propose constructing a joint Hankel matrix along both echo and shot dimensions to improve the reconstruction.Experimental results on in vivo multi-echo data demonstrate that, by performing joint reconstruction along with both echo and shot dimensions, reconstruction accuracy is improved compared to standard 3D-BUDA reconstruction. CAIPI sampling is further shown to enhance image quality. For T 2 * $$ {\mathrm{T}}_2^{\ast } $$ mapping, parameter values from 3D-Joint-CAIPI-BUDA and reference multi-echo GRE are within limits of agreement as quantified by Bland-Altman analysis.The proposed technique enables rapid 3D distortion-free high-resolution imaging and T 2 * $$ {\mathrm{T}}_2^{\ast } $$ mapping. Specifically, 3D-BUDA enables 1-mm isotropic whole-brain imaging in 22 s at 3T and 9 s on a 7T scanner. The combination of multi-echo 3D-BUDA with CAIPI acquisition and joint reconstruction enables distortion-free whole-brain T 2 * $$ {\mathrm{T}}_2^{\ast } $$ mapping in 47 s at 1.1 × 1.1 × 1.0 mm3 resolution.

    View details for DOI 10.1002/mrm.29578

    View details for PubMedID 36705076

  • Optimized three-dimensional ultrashort echo time: Magnetic resonance fingerprinting for myelin tissue fraction mapping. Human brain mapping Zhou, Z., Li, Q., Liao, C., Cao, X., Liang, H., Chen, Q., Pu, R., Ye, H., Tong, Q., He, H., Zhong, J. 2023


    Quantitative assessment of brain myelination has gained attention for both research and diagnosis of neurological diseases. However, conventional pulse sequences cannot directly acquire the myelin-proton signals due to its extremely short T2 and T2* values. To obtain the myelin-proton signals, dedicated short T2 acquisition techniques, such as ultrashort echo time (UTE) imaging, have been introduced. However, it remains challenging to isolate the myelin-proton signals from tissues with longer T2. In this article, we extended our previous two-dimensional ultrashort echo time magnetic resonance fingerprinting (UTE-MRF) with dual-echo acquisition to three dimensional (3D). Given a relatively low proton density (PD) of myelin-proton, we utilized Cramér-Rao Lower Bound to encode myelin-proton with the maximal SNR efficiency for optimizing the MR fingerprinting design, in order to improve the sensitivity of the sequence to myelin-proton. In addition, with a second echo of approximately 3 ms, myelin-water component can be also captured. A myelin-tissue (myelin-proton and myelin-water) fraction mapping can be thus calculated. The optimized 3D UTE-MRF with dual-echo acquisition is tested in simulations, physical phantom and in vivo studies of both healthy subjects and multiple sclerosis patients. The results suggest that the rapidly decayed myelin-proton and myelin-water signal can be depicted with UTE signals of our method at clinically relevant resolution (1.8 mm isotropic) in 15 min. With its good sensitivity to myelin loss in multiple sclerosis patients demonstrated, our method for the whole brain myelin-tissue fraction mapping in clinical friendly scan time has the potential for routine clinical imaging.

    View details for DOI 10.1002/hbm.26203

    View details for PubMedID 36629336

  • Blip up-down acquisition for spin- and gradient-echo imaging (BUDA-SAGE) with self-supervised denoising enables efficient T2 , T2 *, para- and dia-magnetic susceptibility mapping. Magnetic resonance in medicine Zhang, Z., Cho, J., Wang, L., Liao, C., Shin, H. G., Cao, X., Lee, J., Xu, J., Zhang, T., Ye, H., Setsompop, K., Liu, H., Bilgic, B. 2022


    To rapidly obtain high resolution T2 , T2 *, and quantitative susceptibility mapping (QSM) source separation maps with whole-brain coverage and high geometric fidelity.We propose Blip Up-Down Acquisition for Spin And Gradient Echo imaging (BUDA-SAGE), an efficient EPI sequence for quantitative mapping. The acquisition includes multiple T2 *-, T2 '-, and T2 -weighted contrasts. We alternate the phase-encoding polarities across the interleaved shots in this multi-shot navigator-free acquisition. A field map estimated from interim reconstructions was incorporated into the joint multi-shot EPI reconstruction with a structured low rank constraint to eliminate distortion. A self-supervised neural network (NN), MR-Self2Self (MR-S2S), was used to perform denoising to boost SNR. Using Slider encoding allowed us to reach 1 mm isotropic resolution by performing super-resolution reconstruction on volumes acquired with 2 mm slice thickness. Quantitative T2 (=1/R2 ) and T2 * (=1/R2 *) maps were obtained using Bloch dictionary matching on the reconstructed echoes. QSM was estimated using nonlinear dipole inversion on the gradient echoes. Starting from the estimated R2 /R2 * maps, R2 ' information was derived and used in source separation QSM reconstruction, which provided additional para- and dia-magnetic susceptibility maps.In vivo results demonstrate the ability of BUDA-SAGE to provide whole-brain, distortion-free, high-resolution, multi-contrast images and quantitative T2 /T2 * maps, as well as yielding para- and dia-magnetic susceptibility maps. Estimated quantitative maps showed comparable values to conventional mapping methods in phantom and in vivo measurements.BUDA-SAGE acquisition with self-supervised denoising and Slider encoding enables rapid, distortion-free, whole-brain T2 /T2 * mapping at 1 mm isotropic resolution under 90 s.

    View details for DOI 10.1002/mrm.29219

    View details for PubMedID 35436357

  • Optimized multi-axis spiral projection MR fingerprinting with subspace reconstruction for rapid whole-brain high-isotropic-resolution quantitative imaging. Magnetic resonance in medicine Cao, X., Liao, C., Iyer, S. S., Wang, Z., Zhou, Z., Dai, E., Liberman, G., Dong, Z., Gong, T., He, H., Zhong, J., Bilgic, B., Setsompop, K. 2022


    PURPOSE: To improve image quality and accelerate the acquisition of 3D MR fingerprinting (MRF).METHODS: Building on the multi-axis spiral-projection MRF technique, a subspace reconstruction with locally low-rank constraint and a modified spiral-projection spatiotemporal encoding scheme called tiny golden-angle shuffling were implemented for rapid whole-brain high-resolution quantitative mapping. Reconstruction parameters such as the locally low-rank regularization parameter and the subspace rank were tuned using retrospective in vivo data and simulated examinations. B0 inhomogeneity correction using multifrequency interpolation was incorporated into the subspace reconstruction to further improve the image quality by mitigating blurring caused by off-resonance effect.RESULTS: The proposed MRF acquisition and reconstruction framework yields high-quality 1-mm isotropic whole-brain quantitative maps in 2min at better quality compared with 6-min acquisitions of prior approaches. The proposed method was validated to not induce bias in T1 and T2 mapping. High-quality whole-brain MRF data were also obtained at 0.66-mm isotropic resolution in 4min using the proposed technique, where the increased resolution was shown to improve visualization of subtle brain structures.CONCLUSIONS: The proposed tiny golden-angle shuffling, MRF with optimized spiral-projection trajectory and subspace reconstruction enables high-resolution quantitative mapping in ultrafast acquisition time.

    View details for DOI 10.1002/mrm.29194

    View details for PubMedID 35199877