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arXiv 2024年

作者： Diaz, Ernesto Sriram, Renuka Gordon, Jeremy W. Sinha, Avantika Liu, Xiaoxi Sahin, Sule Crane, Jason Olson, Marram P. Chen, Hsin-Yu Bernard, Jenna Vigneron, Daniel B. Wang, Zhen Jane Xu, Duan Larson, Peder E.Z. Department of Radiology and Biomedical Imaging University of California - San Francisco San FranciscoCA United States UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley United States University of California San FranciscoCA United States

Hyperpolarized (HP) 13C MRI has shown promise as a valuable modality for in vivo measurements of metabolism and is currently in human trials at 15 research sites worldwide. With this growth it is important to adopt standardized data storage practices as it will allow sites to meaningfully compare data. In this paper we (1) describe data that we believe should be stored and (2) demonstrate pipelines and methods that utilize the Digital Imaging and Communications in Medicine (DICOM) standard. This includes proposing a set of minimum set of information that is specific to HP 13C MRI studies. We then show where the majority of these can be fit into existing DICOM Attributes, primarily via the "Contrast/Bolus" module. We also demonstrate pipelines for utilizing DICOM for HP 13C MRI. DICOM is the most common standard for clinical medical image storage and provides the flexibility to accommodate the unique aspects of HP 13C MRI, including the HP agent information but also spectroscopic and metabolite dimensions. The pipelines shown include creating DICOM objects for studies on human and animal imaging systems with various pulse sequences. We also show a python-based method to efficiently modify DICOM objects to incorporate the unique HP 13C MRI information that is not captured by existing pipelines. Moreover, we propose best practices for HP 13C MRI data storage that will support future multi-site trials, research studies and technical developments of this imaging technique. © 2024, CC BY.

关键词： Magnetic resonance imaging

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Attenuation coefficient estimation for PET/MRI with Bayesian deep learning pseudo-CT and maximum likelihood estimation of activity and attenuation

arXiv

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arXiv 2020年

作者： Leynes, Andrew Palmera Ahn, sangtae P. Wangerin, Kristen A. Kaushik, sandeep S. Wiesinger, Florian Hope, Thomas A. Larson, Peder E.Z. The Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA94158 United States The UC Berkeley Joint Graduate Program in Bioengineering BerkeleyCA United States UC San Francisco Joint Graduate Program in Bioengineering San FranciscoCA United States GE Research NiskayunaNY United States GE Healthcare WaukeshaWI United States GE Healthcare Munich Germany The Department of Computer Science Technical University of Munich Munich Germany The Department of Radiology San Francisco VA Medical Center San FranciscoCA United States

A major remaining challenge for magnetic resonance-based attenuation correction methods (MRAC) is their susceptibility to sources of MRI artifacts (e.g. implants, motion) and uncertainties due to the limitations of MRI contrast (e.g. accurate bone delineation and density, and separation of air/bone). We propose using a Bayesian deep convolutional neural network that, in addition to generating an initial pseudo-CT from MR data, also produces uncertainty estimates of the pseudo-CT to quantify the limitations of the MR data. These outputs are combined with MLAA reconstruction that uses the PET emission data to improve the attenuation maps. With the proposed approach (UpCT-MLAA), we demonstrate accurate estimation of PET uptake in pelvic lesions and show recovery of metal implants. In patients without implants, UpCT-MLAA had acceptable but slightly higher RMSE than Zero-echo-time and Dixon Deep pseudo-CT when compared to CTAC. In patients with metal implants, MLAA recovered the metal implant;however, anatomy outside the implant region was obscured by noise and crosstalk artifacts. Attenuation coefficients from the pseudo-CT from Dixon MRI were accurate in normal anatomy;however, the metal implant region was estimated to have attenuation coefficients of air. UpCT-MLAA estimated attenuation coefficients of metal implants alongside accurate anatomic depiction outside of implant regions. © 2020, CC BY.

关键词： Magnetic resonance

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A metabolite specific 3D stack-of-spiral bSSFP sequence for improved lactate imaging in hyperpolarized [1-13C]pyruvate studies on a 3T clinical scanner

arXiv

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arXiv 2020年

作者： Tang, Shuyu Bok, Robert Qin, Hecong Reed, Galen VanCriekinge, Mark santos, Romelyn Delos Overall, William santos, Juan Gordon, Jeremy Wang, Zhen Jane Vigneron, Daniel B. Larson, Peder E.Z. UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco University of California Berkeley United States Department of Radiology and Biomedical Imaging University of California - San Francisco San FranciscoCA United States HeartVista Los AltosCA United States

Purpose: The balanced steady-state free precession sequence has been previously explored to improve the efficient use of non-recoverable hyperpolarized 13C magnetization, but suffers from poor spectral selectivity and long acquisition time. The purpose of this study was to develop a novel metabolite-specific 3D bSSFP ("MS-3DSSFP") sequence with stack-of-spiral readouts for improved lactate imaging in hyperpolarized [1-13C]pyruvate studies on a clinical 3T scanner. Methods: Simulations were performed to evaluate the spectral response of the MS-3DSSFP sequence. Thermal 13C phantom experiments were performed to validate the MS-3DSSFP sequence. In vivo hyperpolarized [1-13C]pyruvate studies were performed to compare the MS-3DSSFP sequence with metabolite specific gradient echo ("MS-GRE") sequences for lactate imaging. Results: Simulations, phantom and in vivo studies demonstrate that the MS-3DSSFP sequence achieved spectrally selective excitation on lactate while minimally perturbing other metabolites. Compared with MS-GRE sequences, the MS-3DSSFP sequence showed approximately a 2.5-fold SNR improvement for lactate imaging in rat kidneys, prostate tumors in a mouse model and human kidneys. Conclusions: Improved lactate imaging using the MS-3DSSFP sequence in hyperpolarized [1-13C]pyruvate studies was demonstrated in animals and humans. The MS-3DSSFP sequence could be applied for other clinical applications such as in the brain or adapted for imaging other metabolites such as pyruvate and bicarbonate. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Calibrationless parallel imaging reconstruction based on structured low-rank matrix completion

Calibrationless parallel imaging reconstruction based on str...

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作者： Shin, Peter J. Larson, Peder E. Z. Ohliger, Michael A. Elad, Michael Pauly, John M. Vigneron, Daniel B. Lustig, Michael Department of Radiology and Biomedical Imaging University of California at San Francisco San FranciscoCA United States UC Berkeley-UCSF Graduate Program in Bioengineering CA United States Department of Electrical Engineering and Computer Science University of California at Berkeley BerkeleyCA United States Department of Computer Science Technion'Israel Institute of Technology Haifa Israel Magnetic Resonance Systems Research Laboratory Department of Electrical Engineering Stanford University StanfordCA United States

Purpose: A calibrationless parallel imaging reconstruction method, termed simultaneous autocalibrating and k-space estimation (SAKE), is presented. It is a data-driven, coil-by-coil reconstruction method that does not require a separate calibration step for estimating coil sensitivity information. Methods: In SAKE, an undersampled, multichannel dataset is structured into a single data matrix. The reconstruction is then formulated as a structured low-rank matrix completion problem. An iterative solution that implements a projection-ontosets algorithm with singular value thresholding is described. Results: Reconstruction results are demonstrated for retrospectively and prospectively undersampled, multichannel Cartesian data having no calibration signals. Additionally, non-Cartesian data reconstruction is presented. Finally, improved image quality is demonstrated by combining SAKE with wavelet-based compressed sensing. Conclusion: Because estimation of coil sensitivity information is not needed, the proposed method could potentially benefit MR applications where acquiring accurate calibration data is limiting or not possible at all. © 2013 Wiley Periodicals, Inc.

关键词： Compressed sensing

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A Regional bolus tracking and Real-time B1 Calibration method for Hyperpolarized 13C MRI

arXiv

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arXiv 2020年

作者： Tang, Shuyu Milshteyn, Eugene Reed, Galen Gordon, Jeremy Bok, Robert Zhu, Xucheng Zhu, Zihan Vigneron, Daniel B. Larson, Peder E.Z. UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco United States University of California Berkeley United States Department of Radiology and Biomedical Imaging University of California - San Francisco San FranciscoCA United States HeartVista Los AltosCA United States

Purpose: Acquisition timing and B1 calibration are two key factors that affect the quality and accuracy of hyperpolarized 13C 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 13C metabolites in ***: 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 13C imaging was tested on healthy rats, tumor-bearing mice and a healthy volunteer on a clinical 3T scanner following hyperpolarized [1-13C]pyruvate injection. Multichannel receive coils were used in the human ***: 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 ***: 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 13C imaging. Copyright © 2020, The Authors. All rights reserved.

关键词： Mapping

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Energy dependent systematic errors in dual-energy X-ray CT

Energy dependent systematic errors in dual-energy X-ray CT

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： K.L. Goh S.C. Liew B.H. Hasegawa Department of Physics National University of Singapore Singapore Program in Computational Science National University of Singapore Singapore Department of Radiology and Bioengineering Graduate Group University of California San Francisco USA

Dual-energy X-ray Computed Tomography (DECT) is a technique which is designed to allow the determination of energy-independent material properties. In this study, results of computer simulation show that energy-dependent systematic errors exist in the values of attenuation coefficient synthesized using the basis material decomposition technique with acrylic and aluminum as the basis materials, especially when iodine (e.g., from radiographic contrast media) is present in the body. The errors are reduced when acrylic and an iodine-water mixture are used as the basis materials. The authors propose a simple model for the calculation of energy-dependent systematic errors using effective energies at the lower and higher energy windows of the X-ray spectrum used in the DECT system. The calculated errors agree well with the errors observed in the simulation. These results suggest that the observed systematic errors are predominantly due to the energy dependence of the basis material coefficients.

关键词： Attenuation Aluminum Computed tomography Computational modeling X-ray imaging Material properties Radiography Computer errors Physics computing Radiology

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Noise in ML-EM reconstruction of SPECT images with attenuation correction

Noise in ML-EM reconstruction of SPECT images with attenuati...

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： S.C. Liew Y.K. Ng B.H. Hasegawa Program in Computational Science National University of Singapore Singapore Department of Physics National University of Singapore Singapore Department of Radiology and Bioengineering Graduate Group University of California San Francisco USA

The authors derive a closed form expression for the pixel variance in the iterative ML-EM reconstruction of a uniform circular source embedded in a uniformly attenuating circular object. The derivation includes both the photon noise in the projection data and the noise in the attenuation map used for attenuation correction. The variance is found to increase with the number of iterations, but converges to a finite value. The noise to signal ratio at convergence is the sum of two terms which correspond to the contributions from the photon noise in the projection data and the attenuation map noise. The noise component due to the photon noise varies inversely with the total number of detected counts in the projection data. The relative variance at infinite iterations is similar in magnitude to that obtained for the filtered backprojection algorithm. The component due to attenuation map noise is proportional to the relative variance of the attenuation coefficient in the attenuation map. These observations are consistent with the results of the authors' previous computer simulation and experimental studies.

关键词： Image reconstruction Attenuation Iterative algorithms Single photon emission computed tomography Signal to noise ratio Computer simulation Uncertainty Embedded computing Physics computing Radiology

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Chemical shift separation with controlled aliasing for hyperpolarized 13C metabolic imaging

Chemical shift separation with controlled aliasing for hyper...

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作者： Shin, Peter J. Larson, Peder E.Z. Uecker, Martin Reed, Galen D. Kerr, Adam B. Tropp, James Ohliger, Michael A. Nelson, Sarah J. Pauly, John M. Lustig, Michael Vigneron, Daniel B. Department of Radiology and Biomedical Imaging University of California at San Francisco 1700 4th Street San FranciscoCA94158 United States UC Berkeley - UCSF Graduate Program in Bioengineering CA United States Department of Electrical Engineering and Computer Sciences University of California at Berkeley BerkeleyCA United States Magnetic Resonance Systems Research Laboratory Department of Electrical Engineering Stanford University StanfordCA United States General Electric Healthcare FremontCA United States

Purpose A chemical shift separation technique for hyperpolarized 13C metabolic imaging with high spatial and temporal resolution was developed. Specifically, a fast three-dimensional pulse sequence and a reconstruction method were implemented to acquire signals from multiple 13C species simultaneously with subsequent separation into individual images. Theory and Methods A stack of flyback echo-planar imaging readouts and a set of multiband excitation radiofrequency pulses were designed to spatially modulate aliasing patterns of the acquired metabolite images, which translated the chemical shift separation problem into parallel imaging reconstruction problem. An eight-channel coil array was used for data acquisition and a parallel imaging method based on nonlinear inversion was developed to separate the aliased images. Results Simultaneous acquisitions of pyruvate and lactate in a phantom study and in vivo rat experiments were performed. The results demonstrated successful separation of the metabolite distributions into individual images having high spatial resolution. Conclusion This method demonstrated the ability to provide accelerated metabolite imaging in hyperpolarized 13C MR using multichannel coils, tailored readout, and specialized RF pulses. © 2014 Wiley Periodicals, Inc.

关键词： Separation

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V2a interneuron differentiation from mouse and human pluripotent stem cells (vol 74, pg 897, 2019)

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NATURE PROTOCOLS 2020年第1期15卷 181-181页

作者： Butts, Jessica C. Iyer, Nisha White, Nick Thompson, Russell Sakiyama-Elbert, Shelly McDevitt, Todd C. Gladstone Institutes San Francisco USA Graduate Program in Bioengineering University of California San Francisco and University of California Berkeley USA Department of Biomedical Engineering University of Wisconsin–Madison Madison USA Department of Biomedical Engineering University of Texas at Austin Austin USA Department of Biomedical Engineering Washington University in St. Louis St. Louis USA Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco USA

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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Statistical appearance modeling of whole-body bone shape and density

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Journal of Orthopaedic Translation 2014年第4期2卷 246-247页

作者： Bennett K. Ng Louise Marquino Viva W. Tai Caitlin Sheets Kathleen Mulligan Timothy F. Cootes John A. Shepherd University of California Berkeley–University of California San Francisco Graduate Program in Bioengineering San Francisco California United States of America Department of Radiology and Biomedical Imaging University of California San Francisco United States of America Division of Endocrinology and Metabolism Department of Medicine University of California San Francisco United States of America Clinical and Translational Science Institute University of California San Francisco United States of America Centre for Imaging Sciences Institute of Population Health The University of Manchester Manchester United Kingdom

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