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arXiv 2019年

作者： Ong, Frank Zhu, Xucheng Cheng, Joseph Y. Johnson, Kevin M. Larson, Peder E.Z. Vasanawala, Shreyas S. Lustig, Michael Stanford University CA United States UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco University of California BerkeleyCA United States University of Wisconsin MadisonWI United States University of California San FranciscoCA United States

Purpose: To develop a framework to reconstruct large-scale volumetric dynamic MRI from rapid continuous and non-gated acquisitions, with applications to pulmonary and dynamic contrast enhanced (DCE) imaging. Theory and Methods: The problem considered here is a reconstruction of hundred-gigabytes of dynamic volumetric image data from a few gigabytes of k-space data, acquired continuously over several minutes. This is a vastly under-determined optimization, with problem sizes heavily stressing compute resources as well as memory management and storage. To overcome these challenges, we leverage intrinsic three dimensional (3D) trajectories, such as 3D radial and 3D cones, with ordering that incoherently cover time and k-space over the entire acquisition. We then propose two innovations: (1) A compressed representation using multi-scale low rank matrix factorization that both constrains the reconstruction problem and reduces its memory footprint. (2) Stochastic optimization to reduce computation, improve memory locality and minimize communications between threads and processors. We demonstrate the feasibility of the proposed method on DCE imaging acquired with a golden-angle ordered 3D cones trajectory and pulmonary imaging acquired with a bit-reversed ordered 3D radial trajectory. We compare it with "soft-gated" dynamic reconstruction for DCE and respiratory resolved reconstruction for pulmonary imaging. Results: The proposed technique shows transient dynamics that are not seen in gating based methods. When applied to datasets with irregular, or non-repetitive motions, the proposed method also displays sharper image features. Conclusion: We demonstrated a method that can reconstruct massive 3D dynamic image series in the extreme undersampling and extreme computation setting. Copyright © 2019, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Performance Evaluation and Comparison of two Triple-nuclear RF Resonators for 1H/19F/31P MR Imaging at 9.4T

Performance Evaluation and Comparison of two Triple-nuclear ...

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IEEE International Conference on Real-time Computing and Robotics (RCAR)

作者： Feng Du Shengping Liu Nan Li Congcong Liu Qiaoyan Chen Shuai Zhang Haifeng Wang Xiaoliang Zhang Ye Li Chongqing University of Technology Chongqing Chongqing China Lauterbur Research Center for Biomedical Imaging Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen Guang Dong China UCSF/UC Berkeley Joint Graduate Group in Bioengineering San Francisco CA USA

ISBN: (数字)9781728137261

ISBN: (纸本)9781728137278

Radio frequency (RF) coils are critical devices in magnetic resonance (MR) systems for transmitting and receiving magnetic resonance signals. However, the required high operating frequency at ultrahigh magnetic fields makes the design of highly efficient radio frequency (RF) transmit or receive coils technically challenging. This is particularly true in the double-tuned or triple-tuned RF coils usually required in heteronuclear MRI and MRS where multiple nuclei, such as 1 H, 19 F, and 31 P, are involved. The performance of RF coils is a critically important factor for realizing the high sensitivity provided by ultrahigh magnetic fields to contribute towards the advancement of a novel human in vivo application at 9.4T. In this work, two different configurations of novel triple-nuclear ( 1 H/ 19 F/ 31 P) RF resonators were proposed for the ultrahigh field 9.4T applications. We also reported on the design and construction, and a field-circuit co-simulation was used to obtain the S-parameters, B 1 + field and specific absorption rate (SAR) distributions to evaluate and compare their performance. And the characteristics and advantages of the proposed two different configurations of triple-nuclear RF resonators in the applications of 1 H/ 19 F/ 31 P at ultrahigh magnetic field were investigated.

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Iterative Motion Compensation reconstruction ultra-short TE(iMoCo UTE) for high resolution free breathing pulmonary MRI

arXiv

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arXiv 2020年

作者： Zhu, Xucheng Chan, Marilynn Lustig, Michael Johnson, Kevin Larson, Peder E.Z. UCSF/UC Berkeley Graduate Program in Bioengineering University of California San Francisco San FranciscoCA United States Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA United States Department of Pediatrics Division of Pediatric Pulmonology University of California San Francisco San FranciscoCA United States Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA United States Department of Medical Physics University of Wisconsin Madison MadisonWI United States Department of Radiology University of Wisconsin Madison MadisonWI United States

Purpose: To develop a high scanning efficiency, motion corrected imaging strategy for free-breathing pulmonary MRI by combining a motion compensation reconstruction with a UTE acquisition, called iMoCo UTE. Methods: An optimized golden angle ordering radial UTE sequence was used to continuously acquire data for 5 minutes. All readouts were grouped to different respiratory motion states based on self-navigator signals, then motion resolved data was reconstructed by XD Golden-angle RAdial Sparse Parallel reconstruction (XD-GRASP). One state from the motion resolved images was selected as a reference, and motion fields from the other states to the reference were derived via non-rigid registration. Finally, all motion resolved data and motion fields were reconstructed by using an iterative motion compensation reconstruction with a total generalized variation sparse constraint. Results: The iMoCo UTE strategy was evaluated in volunteers and non-sedated pediatric patient(4-6 y/o) studies. Images reconstructed with iMoCo UTE provided sharper anatomical lung structures, and higher apparent SNR and CNR, compared to using other motion correction strategies, such as soft-gating, motion resolved reconstruction, and non-rigid motion compensation(MoCo). iMoCo UTE also showed promising results in an infant study. Conclusions: The proposed iMoCo UTE combines self-navigation, motion modeling, and a compressed sensing reconstruction to increase scan efficiency, SNR, and reduce respiratory motion in lung MRI. This proposed strategy shows improvements in free breathing lung MRI scans, especially in very challenging application situations, such as pediatric MRI studies. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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A comparison of coil combination strategies in 3D multi-channel MRSI reconstruction for patients with brain tumors (vol 31, e3929, 2018)

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NMR IN BIOMEDICINE 2018年第12期31卷 e3929-e3929页

作者： Vareth, M. Lupo, J. M. Larson, P. E. Z. Nelson, S. J. UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA

The goal of this study was to find the most robust algorithm for a phase‐sensitive coil combination of 3D single‐cycle and lactate‐edited, multi‐channel H‐1 point‐resolved spectroscopy (PRESS) localized echo planar spectroscopic imaging (EPSI) data for clinical applications in the brain. Data were acquired over 5-10 minutes at 3T using 8‐ or 32‐channel array coils. Peak referencing with residual water and N‐acetyl‐aspartate, first‐point phasing, generalized least squared (GLS) and whitened singular‐value decomposition (WSVD) combination algorithms were evaluated relative to unsuppressed water with data from a phantom, six volunteers and 55 patients with brain tumors. Comparison metrics were signal‐to‐noise ratio, coefficient of variance and percent signal increase. Where residual water was present, using it as a reference peak for phasing and weighting factors from an imaging calibration scan gave the best overall performance. Greater improvement was seen for large selected volumes (>720 cm³) and for the 32‐channel array (25%) compared with the 8‐channel array (19%). Applying voxel‐by‐voxel phase corrections produced a larger increase in performance for the 32‐ versus 8‐channel coil. We conclude that, for clinically relevant 3D H‐1 PRESS localized EPSI studies, the most robust technique employed individual phase maps generated from high residual water and individual amplitude maps generated from calibration scans.

关键词： coil combination techniques first‐point phasing GLS lactate editing multichannel EPSI peak referencing PRESS localization WSVD

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Novel techniques for large-scale manipulations of cortical networks in non-human primates

Novel techniques for large-scale manipulations of cortical n...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society

作者： Azadeh Yazdan-Shahmorad Daniel B. Silversmith Philip N. Sabes University of California San Francisco San Francisco CA US UC Berkeley – UCSF Graduate Program in Bioengineering San Francisco CA 94158 USA

Optogenetics is a powerful tool that enables millisecond-level control of the activity of specific groups of neurons. Furthermore, it has the great advantage of artifact free recordings. These characteristics make this technique ideal for relating brain function to behavior in animals with great behavioral capabilities such as non-human primates (NHPs). We recently introduced a practical, stable interface for optogenetic stimulation and recording of large-scale cortical circuits in NHPs. Here we present the various potentials of this interface for studying circuits and connectivity at a large-scale and for relating it to behavior.

关键词： Frequency modulation Oscillators Time series analysis Couplings Electrical stimulation

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Current Methods for Hyperpolarized [1-13C]pyruvate MRI Human Studies

arXiv

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arXiv 2023年

作者： Larson, Peder E.Z. Bernard, Jenna M.L. Bankson, James A. Bøgh, Nikolaj Bok, Robert A. Chen, Albert P. Cunningham, Charles H. Gordon, Jeremy Hövener, Jan-Bernd Laustsen, Christoffer Mayer, Dirk McLean, Mary A. Schilling, Franz Slater, James Vanderheyden, Jean-Luc von Morze, Cornelius Vigneron, Daniel B. Xu, Duan Hansen, Esben Søvsø Szocska Miller, Jack Bertelsen, Lotte Bonde Vaeggemose, Michael Lin, Gigin Capozzi, Andrea Fuetterer, Max Chen, Albert Leftin, Avi Schulte, Rolf Rius, Irene Marco Booth, Thomas C. Mishkovsky, Mor Walker, Christopher Michael Keshari, Kayvan Woitek, Ramona Takado, Yuhei Vasquez, Crystal Müller, Christoph Floyd, Joel Grashei, Martin Topping, Geoff van Heijster, Frits Che, Jenny Kim, Yaewon Kurhanewicz, John Ohliger, Michael Sriram, Renuka Chaumeil, Myriam Bock, Michael Schmidt, Andreas Gallagher, Ferdia Chowdhury, Rafat Gong, Yangcan Punwani, Shonit Merritt, Matthew Grist, James Tyler, Damian Khashami, Fatemeh Malloy, Craig Park, Jae Mo Zaha, Vlad Department of Radiology and Biomedical Imaging University of California San FranciscoCA94143 United States UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco United States University of California BerkeleyCA94143 United States Department of Imaging Physics MD Anderson Medical Center HoustonTX United States The MR Research Center Department of Clinical Medicine Aarhus University Aarhus Denmark GE Healthcare Menlo ParkCA United States Sunnybrook Research Institute TorontoON Canada Department of Medical Biophysics University of Toronto TorontoON Canada Kiel University Am Botanischen Garten 14 Kiel24118 Germany Department of Diagnostic Radiology and Nuclear Medicine University of Maryland School of Medicine BaltimoreMD United States Greenebaum Cancer Center University of Maryland School of Medicine BaltimoreMD United States Department of Radiology University of Cambridge Cambridge United Kingdom Cancer Research UK Cambridge Institute University of Cambridge Li Ka Shing Center Cambridge United Kingdom Department of Nuclear Medicine School of Medicine Klinikum Rechts der Isar Technical University of Munich Munich81675 Germany JLVMI Consulting LLC DousmanWI United States Department of Radiology Washington University St. LouisMO United States Aarhus University Aarhus Denmark Chang Gung Memorial Hospital Taoyuan Taiwan Technical University of Denmark Copenhagen Denmark ETH Zurich Zurich Switzerland GE Healthcare WaukeshaWI United States Institute for Bioengineering of Catalonia Barcelona Spain Kings College London London United Kingdom École Polytechnique Fédérale de Lausanne Lausanne Switzerland MD Anderson Cancer Center HoustonTX United States Memorial Sloan Kettering Cancer Center New YorkNY United States Danube Private University Kerns-Stein an der Donau Austria National Institutes for Quantum Science and Technology Chiba Japan National Institutes Health National Cancer Institute Bethe

MRI with hyperpolarized (HP) 13C agents, also known as HP 13C MRI, can measure processes such as localized metabolism that is altered in numerous cancers, liver, heart, kidney diseases, and more. It has been translated into human studies during the past 10 years, with recent rapid growth in studies largely based on increasing availability of hyperpolarized agent preparation methods suitable for use in humans. This paper aims to capture the current successful practices for HP MRI human studies with [1-13C]pyruvate - by far the most commonly used agent, which sits at a key metabolic junction in glycolysis. The paper is divided into four major topic areas: (1) HP 13C-pyruvate preparation, (2) MRI system setup and calibrations, (3) data acquisition and image reconstruction, and (4) data analysis and quantification. In each area, we identified the key components for a successful study, summarized both published studies and current practices, and discuss evidence gaps, strengths, and limitations. This paper is the output of the "HP 13C MRI Consensus Group" as well as the ISMRM Hyperpolarized Media MR and Hyperpolarized Methods & Equipment study groups. It further aims to provide a comprehensive reference for future consensus building as the field continues to advance human studies with this metabolic imaging modality. © 2023, CC BY.

关键词： Magnetic resonance imaging

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Correction to: Toward Automatic Detection of Radiation-Induced Cerebral Microbleeds Using a 3D Deep Residual Network

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Journal of digital imaging 2019年第5期32卷 898页

作者： Yicheng Chen Javier E Villanueva-Meyer Melanie A Morrison Janine M Lupo UCSF-UC Berkeley Graduate Program in Bioengineering San Francisco USA. Department of Radiology and Biomedical Imaging University of California San Francisco San Francisco USA. UCSF-UC Berkeley Graduate Program in Bioengineering San Francisco USA. Janine.Lupo@ucsf.edu. Department of Radiology and Biomedical Imaging University of California San Francisco San Francisco USA. Janine.Lupo@ucsf.edu.

This paper was published inadvertently as open access. It has been corrected online.

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Publisher Correction: Modular and tunable biological feedback control using a de novo protein switch

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Nature 2020年第7798期579卷 E8页

作者： Andrew H Ng Taylor H Nguyen Mariana Gómez-Schiavon Galen Dods Robert A Langan Scott E Boyken Jennifer A Samson Lucas M Waldburger John E Dueber David Baker Hana El-Samad Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA USA. Department of Bioengineering University of California Berkeley Berkeley CA USA. The UC Berkeley-UCSF Graduate Program in Bioengineering UC Berkeley Berkeley CA USA. Cell Design Initiative University of California San Francisco CA USA. Department of Biochemistry University of Washington Seattle WA USA. Institute for Protein Design University of Washington Seattle WA USA. Graduate Program in Biological Physics Structure and Design University of Washington Seattle WA USA. Howard Hughes Medical Institute University of Washington Seattle WA USA. Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA USA. hana.el-samad@ucsf.edu. Cell Design Initiative University of California San Francisco CA USA. hana.el-samad@ucsf.edu. Chan-Zuckerberg Biohub San Francisco CA USA. hana.el-samad@ucsf.edu.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Drug Delivery: Injectable Drug‐Releasing Microporous Annealed Particle Scaffolds for Treating Myocardial Infarction (Adv. Funct. Mater. 43/2020)

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Advanced Functional Materials 2020年第43期30卷

作者： Jun Fang Jaekyung Koh Qizhi Fang Huiliang Qiu Maani M. Archang Mohammad Mahdi Hasani‐Sadrabadi Hiromi Miwa Xintong Zhong Richard Sievers Dong‐Wei Gao Randall Lee Dino Di Carlo Song Li Department of Bioengineering University of California Los Angeles CA 90095 USA Department of Medicine University of California Los Angeles CA 90095 USA Department of Medicine Cardiovascular Research Institute and Institute for Regeneration Medicine University of California San Francisco CA 94143 USA California NanoSystems Institute (CNSI) University of California Los Angeles CA 90095 USA UC Berkeley‐UCSF Graduate Program in Bioengineering University of California San Francisco San Francisco CA 94158 USA Department of Mechanical and Aerospace Engineering University of California Los Angeles CA 90095 USA Jonsson Comprehensive Cancer Centre University of California Los Angeles CA 90024 USA

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Developing a vision for executing scientifically useful virtual biomedical experiments

Developing a vision for executing scientifically useful virt...

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Agent-Directed Simulation Symposium, ADS 2016, Part of the 2016 Spring Simulation Multi-Conference, SpringSim 2016

作者： Petersen, Brenden K. Hunt, C. Anthony UC Berkeley-UCSF Graduate Program in Bioengineering University of California BerkeleyCA United States Department of Bioengineering and Therapeutic Sciences University of California San FranciscoCA United States

ISBN: (纸本)9781510824256

A virtual biomedical experiment (VBE) is a simulation of a wet-lab or clinical biomedical experiment. The goal of VBEs is to provide a scientifically useful method of in silico experimentation that can challenge concrete hypotheses and provide explanatory, mechanistic insight into the referent system. We envision virtual experimentation not as a supplement to traditional wet-lab experimentation, but rather as an essential part of the scientific method itself. The goal of this work is to lay preliminary groundwork for realizing this vision, through outlining requirements and describing agentbased models demonstrative of this vision. VBEs focus on reasoning by analogy;thus, a VBE includes model components analogous to particular relevant aspects of the referent experiment-from hypothesis formation to data analysis, and key concepts in between. We explore five exemplary categories of scientifically useful VBEs;hypothesis, experiment context, living counterparts, experiment agents, and measurements. We discuss how to develop model components of each category in the context of agent-based modeling. We highlight the importance of two overarching requirements: concreteness and modularity. Finally, we demonstrate this vision by describing an in silico liver model that partially fulfills the VBE vision and requirements, including components corresponding to each of the five VBE categories. © 2016 Society for Modeling & Simulation International (SCS).

关键词： Concretes

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