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Open Access Publications from the University of California

Scholarly Works (8 results)

  • Thesis
  • Peer Reviewed
UC San Francisco Electronic Theses and Dissertations (2020)

Magnetic resonance imaging (MRI) is one of the widely used medical imaging modality, since it can provide both structural and functional assessment in a single imaging session.

However, two major challenges should be considered by using MRI for lung imaging. The first challenge is the intrinsic low SNR of H-1 lung MRI due to the low proton density as well as the fast decay of the lung parenchyma signal. And the second challenge is subject motion. To achieve high resolution structural image, MRI requires a long scan time, usually a few minutes or even longer, which make MRI sensitive to subject motion.

To address the first challenge, ultra-short echo time (UTE) MRI sequence is used to capture the lung parenchyma signal before decay.

As for subject motion, two major strategies are widely used. One strategy is fast breath-holding scan, the subjects are asked to hold their breaths for a short duration, and the fast 3D MR sequence would be used to acquire data within that duration. This dissertation proposes a new acquisition scheme based on the standard UTE sequence, which largely increases the encoding efficiency and improves the breath-holding scan images.

The other is free breathing scan with motion correction. The subjects are allowed to breathe during the MR acquisition. After the acquisition, the motion corrupted data would go through the motion correction step to reconstruct the motion free images. In this dissertation, two novel motion corrected reconstruction strategies are proposed to incorporate the motion modeling and compensation into the reconstruction to get high SNR motion corrected 3D and 4D images.

When translating the developed techniques to the clinical studies, specifically for pediatric and neonatal studies, more practical problems need to be considered, such as smaller but finer anatomy to image, the different respiratory patterns of the young subjects etc. This dissertation proposes a 5-minute free breathing UTE MRI strategy to achieve a 3D high resolution motion free lung image for pediatric and neonatal studies.

    Cover page: Advanced H-1 Lung Magnetic Resonance Imaging
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2021)

    Purpose

    Additional spoiler gradients are required in 3D UTE sequences with random view ordering to suppress magnetization refocusing. By leveraging the encoding gradient induced spoiling effect, the spoiler gradients could potentially be reduced or removed to shorten the TR and increase encoding efficiency. An analysis framework is built that models the gradient spoiling effects and a new ordering scheme is proposed for fast 3D UTE acquisition.

    Theory and methods

    UTE signal evolution and spatial encoding gradient induced spoiling effect are derived from the Bloch equations. And the concept is validated in 2D radial UTE simulation. Then an optimized ordering scheme, named reordered 2D golden angle (r2DGA) scheme, for 3D UTE acquisition is proposed. The r2DGA scheme is compared to the sequential and 3D golden angle schemes in both phantom and volunteer studies.

    Results

    The proposed r2DGA ordering scheme was applied to two applications, single breath-holding and free breathing 3D lung MRI. With r2DGA ordering scheme, breath-holding lung MRI scan increased 60% scan efficiency by removing the spoiler gradients and the free breathing scan reduced 20% scan time compared to the 3D golden angle scheme by reducing the spoiler gradients.

    Conclusions

    The proposed r2DGA ordering scheme UTE acquisition reduces the need of spoiler gradients and increases the encoding efficiency, and shows improvements in both breath-holding and free breathing lung MRI applications.
      Cover page: Optimizing trajectory ordering for fast radial ultra-short TE (UTE) acquisitions
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2019)

      Purpose

      To develop a pulse sequence to dynamically measure the ADC of hyperpolarized substrates during their perfusion, metabolic conversion, and transport.

      Methods

      We proposed a slice-selective double spin echo sequence for dynamic hyperpolarized 13 C diffusion-weighted imaging. The proposed pulse sequence was optimized for a high field preclinical scanner through theoretical analysis and simulation. The performance of the method was compared to non-slice-selective double spin echo via in vivo studies. We also validated the sequence for dynamic ADC measurement in both phantom studies and transgenic mouse model of prostate cancer studies.

      Results

      The optimized pulse sequence outperforms the traditional sequence with smaller saturation effects on the magnetization of hyperpolarized compounds that allowed more dynamic imaging frames covering a longer imaging time window. In pre-clinical studies (N = 8), the dynamic hyperpolarized lactate ADC maps of 6 studies in the prostate tumors showed an increase measured ADC over time, which might be related to lactate efflux from the tumor cells.

      Conclusions

      The proposed sequence was validated and shown to improve dynamic diffusion weighted imaging compared to the traditional double spin echo sequence, providing ADC maps of lactate through time.
        Cover page: Dynamic diffusion‐weighted hyperpolarized 13C imaging based on a slice‐selective double spin echo sequence for measurements of cellular transport
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2018)
        Respiratory motion causes misalignments between positron emission tomography (PET) and magnetic resonance (MR)-derived attenuation maps (µ-maps) in addition to artifacts on both PET and MR images in simultaneous PET/MRI for organs such as liver that can experience motion of several centimeters. To address this problem, we developed an efficient MR-based attenuation correction (MRAC) method to generate phase-matched µ-maps for quiescent period PET (PETQ) in abdominal PET/MRI. MRAC data was acquired with CIRcular Cartesian UnderSampling (CIRCUS) sampling during 100 s in free-breathing as an accelerated data acquisition strategy for phase-matched MRAC (MRACPM-CIRCUS). For comparison, MRAC data with raster (Default) k-space sampling was also acquired during 100 s in free-breathing (MRACPM-Default), and used to evaluate MRACPM-CIRCUS as well as un-matched MRAC (MRACUM) that was un-gated. We purposefully oversampled the MRACPM data to ensure we had enough information to capture all respiratory phases to make this comparison as robust as possible. The proposed MRACPM-CIRCUS was evaluated in 17 patients with 68Ga-DOTA-TOC PET/MRI exams, suspected of having neuroendocrine tumors or liver metastases. Effects of CIRCUS sampling for accelerating a data acquisition were evaluated by simulating the data acquisition time retrospectively in increments of 5 s. Effects of MRACPM-CIRCUS on PETQ were evaluated using uptake differences in the liver lesions (n  =  35), compared to PETQ with MRACPM-Default and MRACUM. A Wilcoxon signed-rank test was performed to compare lesion uptakes between the MRAC methods. MRACPM-CIRCUS showed higher image quality compared to MRACPM-Default for the same acquisition times, demonstrating that a data acquisition time of 30 s was reasonable to achieve phase-matched µ-maps. Lesion update differences between MRACPM-CIRCUS (30 s) versus MRACPM-Default (reference, 100 s) were 0.1%  ±  1.4% (range of  -2.7% to 3.2%) and not significant (P  >  .05); while, the differences between MRACUM versus MRACPM-Default were 0.6%  ±  11.4% with a large variation (range of  -37% to 20%) and significant (P  <  .05). In conclusion, we demonstrated that a data acquisition of 30 s achieved phase-matched µ-maps when using specialized CIRCUS data sampling and phase-matched µ-maps improved PETQ quantification significantly.
          Cover page: Developing an efficient phase-matched attenuation correction method for quiescent period PET in abdominal PET/MRI
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2019)

          Purpose

          Acquisition timing and B1 calibration are two key factors that affect the quality and accuracy of hyperpolarized 13 C MRI. The goal of this project was to develop a new approach using regional bolus tracking to trigger Bloch-Siegert B1 mapping and real-time B1 calibration based on regional B1 measurements, followed by dynamic imaging of hyperpolarized 13 C metabolites in vivo.

          Methods

          The proposed approach was implemented on a system which allows real-time data processing and real-time control on the sequence. Real-time center frequency calibration upon the bolus arrival was also added. The feasibility of applying the proposed framework for in vivo hyperpolarized 13 C imaging was tested on healthy rats, tumor-bearing mice and a healthy volunteer on a clinical 3T scanner following hyperpolarized [1-13 C]pyruvate injection. Multichannel receive coils were used in the human study.

          Results

          Automatic acquisition timing based on either regional bolus peak or bolus arrival was achieved with the proposed framework. Reduced blurring artifacts in real-time reconstructed images were observed with real-time center frequency calibration. Real-time computed B1 scaling factors agreed with real-time acquired B1 maps. Flip angle correction using B1 maps results in a more consistent quantification of metabolic activity (i.e, pyruvate-to-lactate conversion, kPL ). Experiment recordings are provided to demonstrate the real-time actions during the experiment.

          Conclusions

          The proposed method was successfully demonstrated on animals and a human volunteer, and is anticipated to improve the efficient use of the hyperpolarized signal as well as the accuracy and robustness of hyperpolarized 13 C imaging.
            Cover page: A regional bolus tracking and real-time B<sub>1</sub> calibration method for hyperpolarized <sup>13</sup> C MRI.
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2019)

            Purpose

            Acquisition timing and B1 calibration are two key factors that affect the quality and accuracy of hyperpolarized 13 C MRI. The goal of this project was to develop a new approach using regional bolus tracking to trigger Bloch-Siegert B1 mapping and real-time B1 calibration based on regional B1 measurements, followed by dynamic imaging of hyperpolarized 13 C metabolites in vivo.

            Methods

            The proposed approach was implemented on a system which allows real-time data processing and real-time control on the sequence. Real-time center frequency calibration upon the bolus arrival was also added. The feasibility of applying the proposed framework for in vivo hyperpolarized 13 C imaging was tested on healthy rats, tumor-bearing mice and a healthy volunteer on a clinical 3T scanner following hyperpolarized [1-13 C]pyruvate injection. Multichannel receive coils were used in the human study.

            Results

            Automatic acquisition timing based on either regional bolus peak or bolus arrival was achieved with the proposed framework. Reduced blurring artifacts in real-time reconstructed images were observed with real-time center frequency calibration. Real-time computed B1 scaling factors agreed with real-time acquired B1 maps. Flip angle correction using B1 maps results in a more consistent quantification of metabolic activity (i.e, pyruvate-to-lactate conversion, kPL ). Experiment recordings are provided to demonstrate the real-time actions during the experiment.

            Conclusions

            The proposed method was successfully demonstrated on animals and a human volunteer, and is anticipated to improve the efficient use of the hyperpolarized signal as well as the accuracy and robustness of hyperpolarized 13 C imaging.
              Cover page: A regional bolus tracking and real‐time B1 calibration method for hyperpolarized 13C MRI
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2019)
              Effective coil combination methods for human hyperpolarized 13C spectroscopy multi-channel data had been relatively unexplored. This study implemented and tested several coil combination methods, including (1) the sum-of-squares (SOS), (2) singular value decomposition (SVD), (3) Roemer method by using reference peak area as a sensitivity map (RefPeak), and (4) Roemer method by using ESPIRiT-derived sensitivity map (ESPIRiT). These methods were evaluated by numerical simulation, thermal phantom experiments, and human cancer patient studies. Overall, the SVD, RefPeak, and ESPIRiT methods demonstrated better accuracy and robustness than the SOS method. Extracting complex pyruvate signal provides an easy and excellent approximation of the coil sensitivity map while maintaining valuable phase information of the coil-combined data.
                Cover page: Coil combination methods for multi-channel hyperpolarized 13C imaging data from human studies
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2020)

                Purpose

                To ameliorate tradeoffs between a fixed spatial resolution and signal-to-noise ratio (SNR) for hyperpolarized 13 C MRI.

                Methods

                In MRI, SNR is proportional to voxel volume but retrospective downsampling or voxel averaging only improves SNR by the square root of voxel size. This can be exploited with a metabolite-selective imaging approach that independently encodes each compound, yielding high-resolution images for the injected substrate and coarser resolution images for downstream metabolites, while maintaining adequate SNR for each. To assess the efficacy of this approach, hyperpolarized [1-13 C]pyruvate data were acquired in healthy Sprague-Dawley rats (n = 4) and in two healthy human subjects.

                Results

                Compared with a constant resolution acquisition, variable-resolution data sets showed improved detectability of metabolites in pre-clinical renal studies with a 3.5-fold, 8.7-fold, and 6.0-fold increase in SNR for lactate, alanine, and bicarbonate data, respectively. Variable-resolution data sets from healthy human subjects showed cardiac structure and neuro-vasculature in the higher resolution pyruvate images (6.0 × 6.0 mm2 for cardiac and 7.5 × 7.5 mm2 for brain) that would otherwise be missed due to partial-volume effects and illustrates the level of detail that can be achieved with hyperpolarized substrates in a clinical setting.

                Conclusion

                We developed a variable-resolution strategy for hyperpolarized 13 C MRI using metabolite-selective imaging and demonstrated that it mitigates tradeoffs between a fixed spatial resolution and SNR for hyperpolarized substrates, providing both high resolution pyruvate and coarse resolution metabolite data sets in a single exam. This technique shows promise to improve future studies by maximizing metabolite SNR while minimizing partial-volume effects from the injected substrate.
                  Cover page: A variable resolution approach for improved acquisition of hyperpolarized 13C metabolic MRI
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