John M. Pauly

All Publications

• Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. International journal of molecular sciences Van Veen, D., Galaz-Montoya, J. G., Shen, L., Baldwin, P., Chaudhari, A. S., Lyumkis, D., Schmid, M. F., Chiu, W., Pauly, J. 2024; 25 (10)

  Abstract

  Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3-20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.

  View details for DOI 10.3390/ijms25105473

  View details for PubMedID 38791508

• Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. bioRxiv : the preprint server for biology Van Veen, D., Galaz-Montoya, J. G., Shen, L., Baldwin, P., Chaudhari, A. S., Lyumkis, D., Schmid, M. F., Chiu, W., Pauly, J. 2024

  Abstract

  Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3 - 20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.

  View details for DOI 10.1101/2024.04.12.589090

  View details for PubMedID 38712113

  View details for PubMedCentralID PMC11071277

• Adapted large language models can outperform medical experts in clinical text summarization. Nature medicine Van Veen, D., Van Uden, C., Blankemeier, L., Delbrouck, J. B., Aali, A., Bluethgen, C., Pareek, A., Polacin, M., Reis, E. P., Seehofnerová, A., Rohatgi, N., Hosamani, P., Collins, W., Ahuja, N., Langlotz, C. P., Hom, J., Gatidis, S., Pauly, J., Chaudhari, A. S. 2024

  Abstract

  Analyzing vast textual data and summarizing key information from electronic health records imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown promise in natural language processing (NLP) tasks, their effectiveness on a diverse range of clinical summarization tasks remains unproven. Here we applied adaptation methods to eight LLMs, spanning four distinct clinical summarization tasks: radiology reports, patient questions, progress notes and doctor-patient dialogue. Quantitative assessments with syntactic, semantic and conceptual NLP metrics reveal trade-offs between models and adaptation methods. A clinical reader study with 10 physicians evaluated summary completeness, correctness and conciseness; in most cases, summaries from our best-adapted LLMs were deemed either equivalent (45%) or superior (36%) compared with summaries from medical experts. The ensuing safety analysis highlights challenges faced by both LLMs and medical experts, as we connect errors to potential medical harm and categorize types of fabricated information. Our research provides evidence of LLMs outperforming medical experts in clinical text summarization across multiple tasks. This suggests that integrating LLMs into clinical workflows could alleviate documentation burden, allowing clinicians to focus more on patient care.

  View details for DOI 10.1038/s41591-024-02855-5

  View details for PubMedID 38413730

  View details for PubMedCentralID 5593724

• Clinical Text Summarization: Adapting Large Language Models Can Outperform Human Experts. Research square Veen, D. V., Uden, C. V., Blankemeier, L., Delbrouck, J. B., Aali, A., Bluethgen, C., Pareek, A., Polacin, M., Reis, E. P., Seehofnerova, A., Rohatgi, N., Hosamani, P., Collins, W., Ahuja, N., Langlotz, C., Hom, J., Gatidis, S., Pauly, J., Chaudhari, A. 2023

  Abstract

  Sifting through vast textual data and summarizing key information from electronic health records (EHR) imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown immense promise in natural language processing (NLP) tasks, their efficacy on a diverse range of clinical summarization tasks has not yet been rigorously demonstrated. In this work, we apply domain adaptation methods to eight LLMs, spanning six datasets and four distinct clinical summarization tasks: radiology reports, patient questions, progress notes, and doctor-patient dialogue. Our thorough quantitative assessment reveals trade-offs between models and adaptation methods in addition to instances where recent advances in LLMs may not improve results. Further, in a clinical reader study with ten physicians, we show that summaries from our best-adapted LLMs are preferable to human summaries in terms of completeness and correctness. Our ensuing qualitative analysis highlights challenges faced by both LLMs and human experts. Lastly, we correlate traditional quantitative NLP metrics with reader study scores to enhance our understanding of how these metrics align with physician preferences. Our research marks the first evidence of LLMs outperforming human experts in clinical text summarization across multiple tasks. This implies that integrating LLMs into clinical workflows could alleviate documentation burden, empowering clinicians to focus more on personalized patient care and the inherently human aspects of medicine.

  View details for DOI 10.21203/rs.3.rs-3483777/v1

  View details for PubMedID 37961377

  View details for PubMedCentralID PMC10635391

• Erratum: "Ultra-low-dose PET reconstruction using generative adversarial network with feature matching and task-specific perceptual loss". Medical physics Ouyang, J., Chen, K. T., Gong, E., Pauly, J., Zaharchuk, G. 2023; 50 (9): 5932

  View details for DOI 10.1002/mp.16601

  View details for PubMedID 37689088

• Noise2Recon: Enabling SNR-robust MRI reconstruction with semi-supervised and self-supervised learning. Magnetic resonance in medicine Desai, A. D., Ozturkler, B. M., Sandino, C. M., Boutin, R., Willis, M., Vasanawala, S., Hargreaves, B. A., Re, C., Pauly, J. M., Chaudhari, A. S. 2023

  Abstract

  PURPOSE: To develop a method for building MRI reconstruction neural networks robust to changes in signal-to-noise ratio (SNR) and trainable with a limited number of fully sampled scans.METHODS: We propose Noise2Recon, a consistency training method for SNR-robust accelerated MRI reconstruction that can use both fully sampled (labeled) and undersampled (unlabeled) scans. Noise2Recon uses unlabeled data by enforcing consistency between model reconstructions of undersampled scans and their noise-augmented counterparts. Noise2Recon was compared to compressed sensing and both supervised and self-supervised deep learning baselines. Experiments were conducted using retrospectively accelerated data from the mridata three-dimensional fast-spin-echo knee and two-dimensional fastMRI brain datasets. All methods were evaluated in label-limited settings and among out-of-distribution (OOD) shifts, including changes in SNR, acceleration factors, and datasets. An extensive ablation study was conducted to characterize the sensitivity of Noise2Recon to hyperparameter choices.RESULTS: In label-limited settings, Noise2Recon achieved better structural similarity, peak signal-to-noise ratio, and normalized-RMS error than all baselines and matched performance of supervised models, which were trained with 14 * $$ 14\times $$ more fully sampled scans. Noise2Recon outperformed all baselines, including state-of-the-art fine-tuning and augmentation techniques, among low-SNR scans and when generalizing to OOD acceleration factors. Augmentation extent and loss weighting hyperparameters had negligible impact on Noise2Recon compared to supervised methods, which may indicate increased training stability.CONCLUSION: Noise2Recon is a label-efficient reconstruction method that is robust to distribution shifts, such as changes in SNR, acceleration factors, and others, with limited or no fully sampled training data.

  View details for DOI 10.1002/mrm.29759

  View details for PubMedID 37427449

• Optimization in the space domain for density compensation with the nonuniform FFT. Magnetic resonance imaging Dwork, N., O'Connor, D., Johnson, E. M., Baron, C. A., Gordon, J. W., Pauly, J. M., Larson, P. E. 2023

  Abstract

  The non-uniform Discrete Fourier Transform algorithm has shown great utility for reconstructing images from non-uniformly spaced samples in the Fourier domain in several imaging modalities. Due to the non-uniform spacing, some correction for the variable density of the samples must be made. Common methods for generating density compensation values are either sub-optimal or only consider a finite set of points in the optimization. This manuscript presents an algorithm for generating density compensation values from a set of Fourier samples that takes into account the point spread function over an entire rectangular region in the image domain. We show that the reconstructed images using the density compensation values of this method are of superior quality when compared to other standard methods. Results are shown with a numerical phantom and with magnetic resonance images of the abdomen and the knee.

  View details for DOI 10.1016/j.mri.2023.03.003

  View details for PubMedID 36934830

• Automated MRI Field of View Prescription from Region of Interest Prediction by Intra-Stack Attention Neural Network. Bioengineering (Basel, Switzerland) Lei, K., Syed, A. B., Zhu, X., Pauly, J. M., Vasanawala, S. V. 2023; 10 (1)

  Abstract

  Manual prescription of the field of view (FOV) by MRI technologists is variable and prolongs the scanning process. Often, the FOV is too large or crops critical anatomy. We propose a deep learning framework, trained by radiologists' supervision, for automating FOV prescription. An intra-stack shared feature extraction network and an attention network are used to process a stack of 2D image inputs to generate scalars defining the location of a rectangular region of interest (ROI). The attention mechanism is used to make the model focus on a small number of informative slices in a stack. Then, the smallest FOV that makes the neural network predicted ROI free of aliasing is calculated by an algebraic operation derived from MR sampling theory. The framework's performance is examined quantitatively with intersection over union (IoU) and pixel error on position and qualitatively with a reader study. The proposed model achieves an average IoU of 0.867 and an average ROI position error of 9.06 out of 512 pixels on 80 test cases, significantly better than two baseline models and not significantly different from a radiologist. Finally, the FOV given by the proposed framework achieves an acceptance rate of 92% from an experienced radiologist.

  View details for DOI 10.3390/bioengineering10010092

  View details for PubMedID 36671663

• SLfRank: Shinnar-Le-Roux Pulse Design with Reduced Energy and Accurate Phase Profiles using Rank Factorization. IEEE transactions on medical imaging Ong, F., Zhong, Z., Liao, C., Lustig, M., Vasanawala, S. S., Pauly, J. M. 2022; PP

  Abstract

  The Shinnar-Le-Roux (SLR) algorithm is widely used to design frequency selective pulses with large flip angles. We improve its design process to generate pulses with lower energy (by as much as 26%) and more accurate phase profiles. Concretely, the SLR algorithm consists of two steps: (1) an invertible transform between frequency selective pulses and polynomial pairs that represent Cayley-Klein (CK) parameters and (2) the design of the CK polynomial pair to match the desired magnetization profiles. Because the CK polynomial pair is bi-linearly coupled, the original algorithm sequentially solves for each polynomial instead of jointly. This results in sub-optimal pulses. Instead, we leverage a convex relaxation technique, commonly used for low rank matrix recovery, to address the bilinearity. Our numerical experiments show that the resulting pulses are almost always globally optimal in practice. For slice excitation, the proposed algorithm results in more accurate linear phase profiles. And in general the improved pulses have lower energy than the original SLR pulses.

  View details for DOI 10.1109/TMI.2022.3231782

  View details for PubMedID 37015710

• Deep Learning-Based Water-Fat Separation from Dual-Echo Chemical Shift-Encoded Imaging. Bioengineering (Basel, Switzerland) Wu, Y., Alley, M., Li, Z., Datta, K., Wen, Z., Sandino, C., Syed, A., Ren, H., Xing, L., Lustig, M., Pauly, J., Vasanawala, S. 2022; 9 (10)

  Abstract

  Conventional water-fat separation approaches suffer long computational times and are prone to water/fat swaps. To solve these problems, we propose a deep learning-based dual-echo water-fat separation method. With IRB approval, raw data from 68 pediatric clinically indicated dual echo scans were analyzed, corresponding to 19382 contrast-enhanced images. A densely connected hierarchical convolutional network was constructed, in which dual-echo images and corresponding echo times were used as input and water/fat images obtained using the projected power method were regarded as references. Models were trained and tested using knee images with 8-fold cross validation and validated on out-of-distribution data from the ankle, foot, and arm. Using the proposed method, the average computational time for a volumetric dataset with ~400 slices was reduced from 10 min to under one minute. High fidelity was achieved (correlation coefficient of 0.9969, l1 error of 0.0381, SSIM of 0.9740, pSNR of 58.6876) and water/fat swaps were mitigated. I is of particular interest that metal artifacts were substantially reduced, even when the training set contained no images with metallic implants. Using the models trained with only contrast-enhanced images, water/fat images were predicted from non-contrast-enhanced images with high fidelity. The proposed water-fat separation method has been demonstrated to be fast, robust, and has the added capability to compensate for metal artifacts.

  View details for DOI 10.3390/bioengineering9100579

  View details for PubMedID 36290546

• A Semi-Blind Calibration and Compensation Method for Dynamic Range Recovery of Low-Power Pre-Amplifiers in MRI Receive Chains. IEEE transactions on medical imaging Vassos, C., Robb, F., Vasanawala, S., Pauly, J., Scott, G. 2022; PP

  Abstract

  To enable wireless MRI receive arrays, per-channel power consumption must be reduced by a significant factor. To address this, a low-power SiGe alternative to industry standard MRI pre-amplifier blocks has been proposed and its impact on imaging performance evaluated in a benchtop environment. The SiGe amplifier reduces power consumption 28x, but exhibits increased non-linearity and reduced dynamic range relative to industry standard amplifiers. This distorts the images, causing reduced contrast and a blurring of fine features. In conjunction with the amplifier, a semi-blind calibration and compensation framework has been proposed to remove artifacts caused by this non-linearity. Requiring the knowledge of the calibration signal bandwidth, the associated peak transmit powers, and the distorted baseband signals, a second non-linearity is constructed that when cascaded with the receive chain produces a linear response. This method was evaluated for both knee and phantom image datasets of peak input power -20dBm with a -40dBm peak input power image as reference. In the benchtop environment, industry standard amplifiers produced input normalized RMSEs of 0.0199 and 0.0310 for phantom and knee datasets, respectively. The low-power SiGe amplifier resulted in RMSEs of 0.0869 and 0.1130 which were reduced to 0.0158 and 0.0168 following compensation, for phantom and knee images respectively. The ability to effectively compensate for this reduced dynamic range encourages further investigation of low-power SiGe amplifiers for power limited MRI receive arrays.

  View details for DOI 10.1109/TMI.2022.3195656

  View details for PubMedID 35914030

• Rapid fat-water separated T1 mapping using a single shot radial inversion-recovery spoiled gradient recalled pulse sequence. NMR in biomedicine Li, Z., Mathew, M., Syed, A. B., Feng, L., Brunsing, R., Pauly, J. M., Vasanawala, S. S. 2022

  Abstract

  T1 mapping is increasingly used in clinical practice and research studies. With limited scan time, existing techniques often have limited spatial resolution, contrast resolution, and slice coverage. High fat concentrations yield complex errors in Look-Locker T1 methods. In this study, a dual-echo 2D radial IR T1 (DEradIR-T1) technique was developed for fast fat/water-separated T1 mapping. The DEradIR-T1 technique was tested in phantoms, 5 volunteers and 28 patients using a 3T clinical MRI scanner. In our study, simulations were performed to analyze the composite (fat + water) and water-only T1 under different echo times (TEs). In standardized phantoms, an inversion-recovery spin echo (IR-SE) sequence with and without fat saturation pulses served as a T1 reference. Parameter mapping with DEradIR-T1 was also assessed in vivo and values were compared with modified Look-Locker inversion recovery (MOLLI). Bland-Altman analysis and two-tailed paired t-test were used to compare the parameter maps from DEradIR-T1 with the references. Simulations of the composite and water-only T1 under different TEs and levels of fat matched the in vivo studies. T1 maps from DEradIR-T1 on a NIST phantom (PComp =0.97) and a Calimetrix fat/water phantom (PWater = 0.56) matched with the references. In vivo T1 was compared with that of MOLLI: R Comp 2 = 0.77 ; R water 2 = 0.72 . In this work, intravoxel fat is found to have a variable, echo-time dependent effect on measured T1 values, and this effect may be mitigated using the proposed DRradIR-T1.

  View details for DOI 10.1002/nbm.4803

  View details for PubMedID 35891586

• A geometry-informed deep learning framework for ultra-sparse 3D tomographic image reconstruction. Computers in biology and medicine Shen, L., Zhao, W., Capaldi, D., Pauly, J., Xing, L. 2022: 105710

  Abstract

  Deep learning affords enormous opportunities to augment the armamentarium of biomedical imaging. However, the pure data-driven nature of deep learning models may limit the model generalizability and application scope. Here we establish a geometry-informed deep learning framework for ultra-sparse 3D tomographic image reconstruction. We introduce a novel mechanism for integrating geometric priors of the imaging system. We demonstrate that the seamless inclusion of known priors is essential to enhance the performance of 3D volumetric computed tomography imaging with ultra-sparse sampling. The study opens new avenues for data-driven biomedical imaging and promises to provide substantially improved imaging tools for various clinical imaging and image-guided interventions.

  View details for DOI 10.1016/j.compbiomed.2022.105710

  View details for PubMedID 35715260

• NeRP: Implicit Neural Representation Learning With Prior Embedding for Sparsely Sampled Image Reconstruction. IEEE transactions on neural networks and learning systems Shen, L., Pauly, J., Xing, L. 2022; PP

  Abstract

  Image reconstruction is an inverse problem that solves for a computational image based on sampled sensor measurement. Sparsely sampled image reconstruction poses additional challenges due to limited measurements. In this work, we propose a methodology of implicit Neural Representation learning with Prior embedding (NeRP) to reconstruct a computational image from sparsely sampled measurements. The method differs fundamentally from previous deep learning-based image reconstruction approaches in that NeRP exploits the internal information in an image prior and the physics of the sparsely sampled measurements to produce a representation of the unknown subject. No large-scale data is required to train the NeRP except for a prior image and sparsely sampled measurements. In addition, we demonstrate that NeRP is a general methodology that generalizes to different imaging modalities such as computed tomography (CT) and magnetic resonance imaging (MRI). We also show that NeRP can robustly capture the subtle yet significant image changes required for assessing tumor progression.

  View details for DOI 10.1109/TNNLS.2022.3177134

  View details for PubMedID 35657845

• A Geometry-Informed Deep Learning Framework for Ultra-Sparse 3D Tomographic Image Reconstruction Shen, L., Zhao, W., Pauly, J., Xing, L. ELSEVIER IRELAND LTD. 2022: S287-S288

  View details for Web of Science ID 000806759200282

• Novel-view X-ray projection synthesis through geometry-integrated deep learning. Medical image analysis Shen, L., Yu, L., Zhao, W., Pauly, J., Xing, L. 2022; 77: 102372

  Abstract

  X-ray imaging is a widely used approach to view the internal structure of a subject for clinical diagnosis, image-guided interventions and decision-making. The X-ray projections acquired at different view angles provide complementary information of patient's anatomy and are required for stereoscopic or volumetric imaging of the subject. In reality, obtaining multiple-view projections inevitably increases radiation dose and complicates clinical workflow. Here we investigate a strategy of obtaining the X-ray projection image at a novel view angle from a given projection image at a specific view angle to alleviate the need for actual projection measurement. Specifically, a Deep Learning-based Geometry-Integrated Projection Synthesis (DL-GIPS) framework is proposed for the generation of novel-view X-ray projections. The proposed deep learning model extracts geometry and texture features from a source-view projection, and then conducts geometry transformationon the geometry features to accommodate the change of view angle.At the final stage, the X-ray projection in the target view is synthesized from the transformed geometry and the shared texture features via an image generator. The feasibility and potential impact of the proposed DL-GIPS model are demonstrated using lung imaging cases.The proposed strategy can be generalized to a general case of multiple projections synthesis from multiple input views and potentially provides a new paradigm for various stereoscopic and volumetric imaging with substantially reduced efforts in data acquisition.

  View details for DOI 10.1016/j.media.2022.102372

  View details for PubMedID 35131701

• Attention-guided deep learning for gestational age prediction using fetal brain MRI. Scientific reports Shen, L., Zheng, J., Lee, E. H., Shpanskaya, K., McKenna, E. S., Atluri, M. G., Plasto, D., Mitchell, C., Lai, L. M., Guimaraes, C. V., Dahmoush, H., Chueh, J., Halabi, S. S., Pauly, J. M., Xing, L., Lu, Q., Oztekin, O., Kline-Fath, B. M., Yeom, K. W. 1800; 12 (1): 1408

  Abstract

  Magnetic resonance imaging offers unrivaled visualization of the fetal brain, forming the basis for establishing age-specific morphologic milestones. However, gauging age-appropriate neural development remains a difficult task due to the constantly changing appearance of the fetal brain, variable image quality, and frequent motion artifacts. Here we present an end-to-end, attention-guided deep learning model that predicts gestational age with R2 score of 0.945, mean absolute error of 6.7days, and concordance correlation coefficient of 0.970. The convolutional neural network was trained on a heterogeneous dataset of 741 developmentally normal fetal brain images ranging from 19 to 39weeks in gestational age. We also demonstrate model performance and generalizability using independent datasets from four academic institutions across the U.S. and Turkey with R2 scores of 0.81-0.90 after minimal fine-tuning. The proposed regression algorithm provides an automated machine-enabled tool with the potential to better characterize in utero neurodevelopment and guide real-time gestational age estimation after the first trimester.

  View details for DOI 10.1038/s41598-022-05468-5

  View details for PubMedID 35082346

• Artifact- and content-specific quality assessment for MRI with image rulers. Medical image analysis Lei, K., Syed, A. B., Zhu, X., Pauly, J. M., Vasanawala, S. S. 1800; 77: 102344

  Abstract

  In clinical practice MR images are often first seen by radiologists long after the scan. If image quality is inadequate either patients have to return for an additional scan, or a suboptimal interpretation is rendered. An automatic image quality assessment (IQA) would enable real-time remediation. Existing IQA works for MRI give only a general quality score, agnostic to the cause of and solution to low-quality scans. Furthermore, radiologists' image quality requirements vary with the scan type and diagnostic task. Therefore, the same score may have different implications for different scans. We propose a framework with multi-task CNN model trained with calibrated labels and inferenced with image rulers. Labels calibrated by human inputs follow a well-defined and efficient labeling task. Image rulers address varying quality standards and provide a concrete way of interpreting raw scores from the CNN. The model supports assessments of two of the most common artifacts in MRI: noise and motion. It achieves accuracies of around 90%, 6% better than the best previous method examined, and 3% better than human experts on noise assessment. Our experiments show that label calibration, image rulers, and multi-task training improve the model's performance and generalizability.

  View details for DOI 10.1016/j.media.2021.102344

  View details for PubMedID 35091278

• Scale-Equivariant Unrolled Neural Networks for Data-Efficient Accelerated MRI Reconstruction Gunel, B., Sahiner, A., Desai, A. D., Chaudhari, A. S., Vasanawala, S., Pilanci, M., Pauly, J., Wang, L., Dou, Q., Fletcher, P. T., Speidel, S., Li, S. SPRINGER INTERNATIONAL PUBLISHING AG. 2022: 737-747

  View details for DOI 10.1007/978-3-031-16446-0_70

  View details for Web of Science ID 000867434800070

• Unraveling Attention via Convex Duality: Analysis and Interpretations of Vision Transformers Sahiner, A., Ergen, T., Ozturkler, B., Pauly, J., Mardani, M., Pilanci, M., Chaudhuri, K., Jegelka, S., Song, L., Szepesvari, C., Niu, G., Sabato, S. JMLR-JOURNAL MACHINE LEARNING RESEARCH. 2022: 19050-19088

  View details for Web of Science ID 000900130200004

• Learned Compression of High Dimensional Image Datasets Cole, E., Meng, Q., Pauly, J., Vasanawala, S., IEEE IEEE. 2022: 1747-1751

  View details for DOI 10.1109/CVPRW56347.2022.00184

  View details for Web of Science ID 000861612701079

• Utilizing the Wavelet Transform's Structure in Compressed Sensing. Signal, image and video processing Dwork, N., O'Connor, D., Baron, C. A., Johnson, E. M., Kerr, A. B., Pauly, J. M., Larson, P. E. 2021; 15 (7): 1407-1414

  Abstract

  Compressed sensing has empowered quality image reconstruction with fewer data samples than previously thought possible. These techniques rely on a sparsifying linear transformation. The Daubechies wavelet transform is commonly used for this purpose. In this work, we take advantage of the structure of this wavelet transform and identify an affine transformation that increases the sparsity of the result. After inclusion of this affine transformation, we modify the resulting optimization problem to comply with the form of the Basis Pursuit Denoising problem. Finally, we show theoretically that this yields a lower bound on the error of the reconstruction and present results where solving this modified problem yields images of higher quality for the same sampling patterns using both magnetic resonance and optical images.

  View details for DOI 10.1007/s11760-021-01872-y

  View details for PubMedID 34531930

  View details for PubMedCentralID PMC8439112

• Biopsy Marker Localization with Thermo-Acoustic Ultrasound for Lumpectomy Guidance. Medical physics Dixit, N., Daniel, B. L., Hargreaves, B. A., Pauly, J. M., Scott, G. C. 2021

  Abstract

  PURPOSE: Almost one in four lumpectomies fails to fully remove cancerous tissue from the breast, requiring reoperation. This high failure rate suggests that existing lumpectomy guidance methods are inadequate for allowing surgeons to consistently identify the proper volume of tissue for excision. Current guidance techniques either provide little information about the tumor position or require surgeons to frequently switch between making incisions and manually probing for a marker placed at the lesion site. This article explores the feasibility of thermo-acoustic ultrasound (TAUS) to enable hands-free localization of metallic biopsy markers throughout surgery, which would allow for continuous visualization of the lesion site in the breast without the interruption of surgery. In a TAUS-based localization system, microwave excitations would be transmitted into the breast, and the amplification in microwave absorption around the metallic markers would generate acoustic signals from the marker sites through the thermo-acoustic effect. Detection and ranging of these signals by multiple acoustic receivers on the breast could then enable marker localization through acoustic multilateration.METHODS: Physics simulations were used to characterize the TAUS signals generated from different markers by microwave excitations. First, electromagnetic simulations determined the spatial pattern of the amplification in microwave absorption around the markers. Then, acoustic simulations characterized the acoustic fields generated from these markers at various acoustic frequencies. TAUS-based one-dimensional (1D) ranging of two metallic markers - including a biopsy marker that is FDA-approved for clinical use - immersed in saline was also performed using a bench-top setup. To perform TAUS acquisitions, a microwave applicator was driven by 2.66 GHz microwave signals that were amplitude-modulated by chirps at the desired acoustic excitation frequencies, and the resulting TAUS signal from the markers was detected by an ultrasonic transducer.RESULTS: The simulation results show that the geometry of the marker strongly impacts the quantity and spatial pattern of both the microwave absorption around the marker and the resulting TAUS signal generated from the marker. The simulated TAUS signal maps and acoustic frequency responses also make clear that the marker geometry plays an important role in determining the overall system response. Using the bench-top setup, TAUS detection and 1D localization of the markers was successfully demonstrated for multiple different combinations of microwave applicator and metallic marker. These initial results indicate that TAUS-based localization of biopsy markers is feasible.CONCLUSIONS: Through microwave excitations and acoustic detection, TAUS can be used to localize metallic biopsy markers. With further development, TAUS opens new avenues to enable a more intuitive lumpectomy guidance system that could help to achieve better lumpectomy outcomes.

  View details for DOI 10.1002/mp.15115

  View details for PubMedID 34287972

• Multi-Domain Image Completion for Random Missing Input Data IEEE TRANSACTIONS ON MEDICAL IMAGING Shen, L., Zhu, W., Wang, X., Xing, L., Pauly, J. M., Turkbey, B., Harmon, S., Sanford, T., Mehralivand, S., Choyke, P. L., Wood, B. J., Xu, D. 2021; 40 (4): 1113–22

  Abstract

  Multi-domain data are widely leveraged in vision applications taking advantage of complementary information from different modalities, e.g., brain tumor segmentation from multi-parametric magnetic resonance imaging (MRI). However, due to possible data corruption and different imaging protocols, the availability of images for each domain could vary amongst multiple data sources in practice, which makes it challenging to build a universal model with a varied set of input data. To tackle this problem, we propose a general approach to complete the random missing domain(s) data in real applications. Specifically, we develop a novel multi-domain image completion method that utilizes a generative adversarial network (GAN) with a representational disentanglement scheme to extract shared content encoding and separate style encoding across multiple domains. We further illustrate that the learned representation in multi-domain image completion could be leveraged for high-level tasks, e.g., segmentation, by introducing a unified framework consisting of image completion and segmentation with a shared content encoder. The experiments demonstrate consistent performance improvement on three datasets for brain tumor segmentation, prostate segmentation, and facial expression image completion respectively.

  View details for DOI 10.1109/TMI.2020.3046444

  View details for Web of Science ID 000637532800002

  View details for PubMedID 33351753

• Utilizing the wavelet transform's structure in compressed sensing SIGNAL IMAGE AND VIDEO PROCESSING Dwork, N., O'Connor, D., Baron, C. A., Johnson, E. M., Kerr, A. B., Pauly, J. M., Larson, P. Z. 2021

  View details for DOI 10.1007/s11760-021-01872-y

  View details for Web of Science ID 000626818000001

• Analysis of deep complex-valued convolutional neural networks for MRI reconstruction and phase-focused applications. Magnetic resonance in medicine Cole, E. n., Cheng, J. n., Pauly, J. n., Vasanawala, S. n. 2021

  Abstract

  Deep learning has had success with MRI reconstruction, but previously published works use real-valued networks. The few works which have tried complex-valued networks have not fully assessed their impact on phase. Therefore, the purpose of this work is to fully investigate end-to-end complex-valued convolutional neural networks (CNNs) for accelerated MRI reconstruction and in several phase-based applications in comparison to 2-channel real-valued networks.Several complex-valued activation functions for MRI reconstruction were implemented, and their performance was compared. Complex-valued convolution was implemented and tested on an unrolled network architecture and a U-Net-based architecture over a wide range of network widths and depths with knee, body, and phase-contrast datasets.Quantitative and qualitative results demonstrated that complex-valued CNNs with complex-valued convolutions provided superior reconstructions compared to real-valued convolutions with the same number of trainable parameters for both an unrolled network architecture and a U-Net-based architecture, and for 3 different datasets. Complex-valued CNNs consistently had superior normalized RMS error, structural similarity index, and peak SNR compared to real-valued CNNs.Complex-valued CNNs can enable superior accelerated MRI reconstruction and phase-based applications such as fat-water separation, and flow quantification compared to real-valued convolutional neural networks.

  View details for DOI 10.1002/mrm.28733

  View details for PubMedID 33724507

• Ultra-low-dose 18F-FDG brain PET/MR denoising using deep learning and multi-contrast information Xu, J., Gong, E., Ouyang, J., Pauly, J., Zaharchuk, G., Isgum, Landman, B. A. SPIE-INT SOC OPTICAL ENGINEERING. 2021

  View details for DOI 10.1117/12.2548350

  View details for Web of Science ID 000672558500056

• Deep learning and multi-contrast based denoising for low-SNR Arterial Spin Labeling (ASL) MRI Gong, E., Guo, J., Liu, J., Fan, A., Pauly, J., Zaharchuk, G., Isgum, Landman, B. A. SPIE-INT SOC OPTICAL ENGINEERING. 2021

  View details for DOI 10.1117/12.2549765

  View details for Web of Science ID 000672558500018

• Fast Unsupervised MRI Reconstruction Without Fully-Sampled Ground Truth Data Using Generative Adversarial Networks Cole, E. K., Ong, F., Vasanawala, S. S., Pauly, J. M., IEEE Comp Soc IEEE COMPUTER SOC. 2021: 3971-3980

  View details for DOI 10.1109/ICCVW54120.2021.00444

  View details for Web of Science ID 000739651104008

• Wasserstein GANs for MR Imaging: From Paired to Unpaired Training IEEE TRANSACTIONS ON MEDICAL IMAGING Lei, K., Mardani, M., Pauly, J. M., Vasanawala, S. S. 2021; 40 (1): 105–15

  Abstract

  Lack of ground-truth MR images impedes the common supervised training of neural networks for image reconstruction. To cope with this challenge, this article leverages unpaired adversarial training for reconstruction networks, where the inputs are undersampled k-space and naively reconstructed images from one dataset, and the labels are high-quality images from another dataset. The reconstruction networks consist of a generator which suppresses the input image artifacts, and a discriminator using a pool of (unpaired) labels to adjust the reconstruction quality. The generator is an unrolled neural network - a cascade of convolutional and data consistency layers. The discriminator is also a multilayer CNN that plays the role of a critic scoring the quality of reconstructed images based on the Wasserstein distance. Our experiments with knee MRI datasets demonstrate that the proposed unpaired training enables diagnostic-quality reconstruction when high-quality image labels are not available for the input types of interest, or when the amount of labels is small. In addition, our adversarial training scheme can achieve better image quality (as rated by expert radiologists) compared with the paired training schemes with pixel-wise loss.

  View details for DOI 10.1109/TMI.2020.3022968

  View details for Web of Science ID 000604883800010

  View details for PubMedID 32915728

  View details for PubMedCentralID PMC7797774

• Uncertainty Quantification in Deep MRI Reconstruction IEEE TRANSACTIONS ON MEDICAL IMAGING Edupuganti, V., Mardani, M., Vasanawala, S., Pauly, J. 2021; 40 (1): 239–50

  Abstract

  Reliable MRI is crucial for accurate interpretation in therapeutic and diagnostic tasks. However, undersampling during MRI acquisition as well as the overparameterized and non-transparent nature of deep learning (DL) leaves substantial uncertainty about the accuracy of DL reconstruction. With this in mind, this study aims to quantify the uncertainty in image recovery with DL models. To this end, we first leverage variational autoencoders (VAEs) to develop a probabilistic reconstruction scheme that maps out (low-quality) short scans with aliasing artifacts to the diagnostic-quality ones. The VAE encodes the acquisition uncertainty in a latent code and naturally offers a posterior of the image from which one can generate pixel variance maps using Monte-Carlo sampling. Accurately predicting risk requires knowledge of the bias as well, for which we leverage Stein's Unbiased Risk Estimator (SURE) as a proxy for mean-squared-error (MSE). A range of empirical experiments is performed for Knee MRI reconstruction under different training losses (adversarial and pixel-wise) and unrolled recurrent network architectures. Our key observations indicate that: 1) adversarial losses introduce more uncertainty; and 2) recurrent unrolled nets reduce the prediction uncertainty and risk.

  View details for DOI 10.1109/TMI.2020.3025065

  View details for Web of Science ID 000604883800021

  View details for PubMedID 32956045

• Synthesize High-Quality Multi-Contrast Magnetic Resonance Imaging From Multi-Echo Acquisition Using Multi-Task Deep Generative Model IEEE TRANSACTIONS ON MEDICAL IMAGING Wang, G., Gong, E., Banerjee, S., Martin, D., Tong, E., Choi, J., Chen, H., Wintermark, M., Pauly, J. M., Zaharchuk, G. 2020; 39 (10): 3089–99

  Abstract

  Multi-echo saturation recovery sequence can provide redundant information to synthesize multi-contrast magnetic resonance imaging. Traditional synthesis methods, such as GE's MAGiC platform, employ a model-fitting approach to generate parameter-weighted contrasts. However, models' over-simplification, as well as imperfections in the acquisition, can lead to undesirable reconstruction artifacts, especially in T2-FLAIR contrast. To improve the image quality, in this study, a multi-task deep learning model is developed to synthesize multi-contrast neuroimaging jointly using both signal relaxation relationships and spatial information. Compared with previous deep learning-based synthesis, the correlation between different destination contrast is utilized to enhance reconstruction quality. To improve model generalizability and evaluate clinical significance, the proposed model was trained and tested on a large multi-center dataset, including healthy subjects and patients with pathology. Results from both quantitative comparison and clinical reader study demonstrate that the multi-task formulation leads to more efficient and accurate contrast synthesis than previous methods.

  View details for DOI 10.1109/TMI.2020.2987026

  View details for Web of Science ID 000574745800010

  View details for PubMedID 32286966

• Rosette Trajectories Enable Ungated, Motion-Robust, Simultaneous Cardiac and Liver T2 * Iron Assessment. Journal of magnetic resonance imaging : JMRI Bush, A. M., Sandino, C. M., Ramachandran, S., Ong, F., Dwork, N., Zucker, E. J., Syed, A. B., Pauly, J. M., Alley, M. T., Vasanawala, S. S. 2020: e27196

  Abstract

  BACKGROUND: Quantitative T2 * MRI is the standard of care for the assessment of iron overload. However, patient motion corrupts T2 * estimates.PURPOSE: To develop and evaluate a motion-robust, simultaneous cardiac and liver T2 * imaging approach using non-Cartesian, rosette sampling and a model-based reconstruction as compared to clinical-standard Cartesian MRI.STUDY TYPE: Prospective.PHANTOM/POPULATION: Six ferumoxytol-containing phantoms (26-288mug/mL). Eight healthy subjects and 18 patients referred for clinically indicated iron overload assessment.FIELD STRENGTH/SEQUENCE: 1.5T, 2D Cartesian and rosette gradient echo (GRE) ASSESSMENT: GRE T2 * values were validated in ferumoxytol phantoms. In healthy subjects, test-retest and spatial coefficient of variation (CoV) analysis was performed during three breathing conditions. Cartesian and rosette T2 * were compared using correlation and Bland-Altman analysis. Images were rated by three experienced radiologists on a 5-point scale.STATISTICAL TESTS: Linear regression, analysis of variance (ANOVA), and paired Student's t-testing were used to compare reproducibility and variability metrics in Cartesian and rosette scans. The Wilcoxon rank test was used to assess reader score comparisons and reader reliability was measured using intraclass correlation analysis.RESULTS: Rosette R2* (1/T2 *) was linearly correlated with ferumoxytol concentration (r2 = 1.00) and not significantly different than Cartesian values (P = 0.16). During breath-holding, ungated rosette liver and heart T2 * had lower spatial CoV (liver: 18.4±9.3% Cartesian, 8.8%±3.4% rosette, P = 0.02, heart: 37.7%±14.3% Cartesian, 13.4%±1.7% rosette, P = 0.001) and higher-quality scores (liver: 3.3 [3.0-3.6] Cartesian, 4.7 [4.1-4.9] rosette, P = 0.005, heart: 3.0 [2.3-3] Cartesian, 4.5 [3.8-5.0] rosette, P = 0.005) compared to Cartesian values. During free-breathing and failed breath-holding, Cartesian images had very poor to average image quality with significant artifacts, whereas rosette remained very good, with minimal artifacts (P = 0.001).DATA CONCLUSION: Rosette k-sampling with a model-based reconstruction offers a clinically useful motion-robust T2 * mapping approach for iron quantification.

  View details for DOI 10.1002/jmri.27196

  View details for PubMedID 32452088

• Two-dimensional UTE overview imaging for dental application. Magnetic resonance in medicine Stumpf, K., Kaye, E., Paul, J., Wundrak, S., Pauly, J. M., Rasche, V. 2020

  Abstract

  PURPOSE: To investigate the applicability of a 2D-UTE half-pulse sequence for dental overview imaging and the detection of signal from mineralized dental tissue and caries lesions with ultra-short T 2 as an efficient alternative to 3D sequences.METHODS: A modified 2D-UTE sequence using 240-s half-pulses for excitation and a reduction of the coil tune delay from the manufacturer preset value allowed for the acquisition of in vivo dental images with a TE of 35 s at 1.5T. The common occurrence of out-of-slice signal for half-pulse sequences was avoided by applying a quadratic-phase saturation pulse before each half-RF excitation. A conventional 2D-UTE sequence with a TE of 750 s, using slice selection rephasing, was used for comparison.RESULTS: Quadratic phase saturation pulses adequately improve the slice profile of half-pulse excitations for dental imaging with a surface coil. In vivo images and SNR measurements show a distinct increase in signal in ultrashort T 2 tissues for the proposed 2D-UTE half-pulse sequence compared with a 2D-UTE sequence using conventional slice selection, leading to an improved detection of caries lesions.CONCLUSION: The proposed pulse sequence enables the acquisition of in vivo images of a comprehensive overview of bone structures and teeth of a single side of the upper and lower jaw and signal detection from mineralized dental tissues in clinically acceptable scan times.

  View details for DOI 10.1002/mrm.28312

  View details for PubMedID 32390153

• Multi-scale Unrolled Deep Learning Framework for Accelerated Magnetic Resonance Imaging. Proceedings. IEEE International Symposium on Biomedical Imaging Nakarmi, U., Cheng, J. Y., Rios, E. P., Mardani, M., Pauly, J. M., Ying, L., Vasanawala, S. S. 2020; 2020: 1056–59

  Abstract

  Accelerating data acquisition in magnetic resonance imaging (MRI) has been of perennial interest due to its prohibitively slow data acquisition process. Recent trends in accelerating MRI employ data-centric deep learning frameworks due to its fast inference time and 'one-parameter-fit-all' principle unlike in traditional model-based acceleration techniques. Unrolled deep learning framework that combines the deep priors and model knowledge are robust compared to naive deep learning based framework. In this paper, we propose a novel multi-scale unrolled deep learning framework which learns deep image priors through multi-scale CNN and is combined with unrolled framework to enforce data-consistency and model knowledge. Essentially, this framework combines the best of both learning paradigms:model-based and data-centric learning paradigms. Proposed method is verified using several experiments on numerous data sets.

  View details for DOI 10.1109/isbi45749.2020.9098684

  View details for PubMedID 33282118

• DIAGNOSTIC IMAGE QUALITY ASSESSMENT AND CLASSIFICATION IN MEDICAL IMAGING: OPPORTUNITIES AND CHALLENGES. Proceedings. IEEE International Symposium on Biomedical Imaging Ma, J. J., Nakarmi, U., Kin, C. Y., Sandino, C. M., Cheng, J. Y., Syed, A. B., Wei, P., Pauly, J. M., Vasanawala, S. S. 2020; 2020: 337-340

  Abstract

  Magnetic Resonance Imaging (MRI) suffers from several artifacts, the most common of which are motion artifacts. These artifacts often yield images that are of non-diagnostic quality. To detect such artifacts, images are prospectively evaluated by experts for their diagnostic quality, which necessitates patient-revisits and rescans whenever non-diagnostic quality scans are encountered. This motivates the need to develop an automated framework capable of accessing medical image quality and detecting diagnostic and non-diagnostic images. In this paper, we explore several convolutional neural network-based frameworks for medical image quality assessment and investigate several challenges therein.

  View details for DOI 10.1109/isbi45749.2020.9098735

  View details for PubMedID 33274013

  View details for PubMedCentralID PMC7710391

• Multi-scale Unrolled Deep Learning Framework for Accelerated Magnetic Resonance Imaging Nakarmi, U., Cheng, J. Y., Rios, E. P., Mardani, M., Pauly, J. M., Ying, L., Vasanawala, S. S., IEEE IEEE. 2020: 1052–55

  View details for Web of Science ID 000578080300214

• Fast variable density Poisson-disc sample generation with directional variation for compressed sensing in MRI. Magnetic resonance imaging Dwork, N. n., Baron, C. A., Johnson, E. M., O'Connor, D. n., Pauly, J. M., Larson, P. E. 2020

  Abstract

  We present a fast method for generating random samples according to a variable density poisson-disc distribution. A minimum parameter value is used to create a background grid array for keeping track of those points that might affect any new candidate point; this reduces the number of conflicts that must be checked before acceptance of a new point, thus reducing the number of computations required. We demonstrate the algorithm's ability to generate variable density poisson-disc sampling patterns according to a parameterized function, including patterns where the variations in density are a function of direction. We further show that these sampling patterns are appropriate for compressed sensing applications. Finally, we present a method to generate patterns with a specific acceleration rate.

  View details for DOI 10.1016/j.mri.2020.11.012

  View details for PubMedID 33232767

• Compressed Sensing: From Research to Clinical Practice With Deep Neural Networks: Shortening Scan Times for Magnetic Resonance Imaging IEEE SIGNAL PROCESSING MAGAZINE Sandino, C. M., Cheng, J. Y., Chen, F., Mardani, M., Pauly, J. M., Vasanawala, S. S. 2020; 37 (1): 117–27

  View details for DOI 10.1109/MSP.2019.2950433

  View details for Web of Science ID 000510210500015

• Compressed Sensing: From Research to Clinical Practice with Deep Neural Networks. IEEE signal processing magazine Sandino, C. M., Cheng, J. Y., Chen, F., Mardani, M., Pauly, J. M., Vasanawala, S. S. 2020; 37 (1): 111-127

  Abstract

  Compressed sensing (CS) reconstruction methods leverage sparse structure in underlying signals to recover high-resolution images from highly undersampled measurements. When applied to magnetic resonance imaging (MRI), CS has the potential to dramatically shorten MRI scan times, increase diagnostic value, and improve overall patient experience. However, CS has several shortcomings which limit its clinical translation such as: 1) artifacts arising from inaccurate sparse modelling assumptions, 2) extensive parameter tuning required for each clinical application, and 3) clinically infeasible reconstruction times. Recently, CS has been extended to incorporate deep neural networks as a way of learning complex image priors from historical exam data. Commonly referred to as unrolled neural networks, these techniques have proven to be a compelling and practical approach to address the challenges of sparse CS. In this tutorial, we will review the classical compressed sensing formulation and outline steps needed to transform this formulation into a deep learning-based reconstruction framework. Supplementary open source code in Python will be used to demonstrate this approach with open databases. Further, we will discuss considerations in applying unrolled neural networks in the clinical setting.

  View details for DOI 10.1109/MSP.2019.2950433

  View details for PubMedID 33192036

  View details for PubMedCentralID PMC7664163

• DIAGNOSTIC IMAGE QUALITY ASSESSMENT AND CLASSIFICATION IN MEDICAL IMAGING: OPPORTUNITIES AND CHALLENGES Ma, J. J., Nakarmi, U., Kin, C., Sandino, C. M., Cheng, J. Y., Syed, A. B., Wei, P., Pauly, J. M., Vasanawala, S. S., IEEE IEEE. 2020: 337–40

  View details for Web of Science ID 000578080300058

• Ultra-low-dose PET Reconstruction using Generative Adversarial Network with Feature Matching and Task-Specific Perceptual Loss. Medical physics Ouyang, J., Chen, K. T., Gong, E., Pauly, J., Zaharchuk, G. 2019

  Abstract

  PURPOSE: Our goal is to use a generative adversarial network (GAN) with feature matching and task-specific perceptual loss to synthesize standard-dose amyloid PET images of high quality and including accurate pathological features from ultra-low-dose PET images only.METHODS: 40 PET datasets from 39 participants were acquired with a simultaneous PET/MRI scanner following injection of 330±30 MBq of the amyloid radiotracer 18F-florbetaben. The raw list-mode PET data were reconstructed as the standard-dose ground truth and were randomly undersampled by a factor of 100 to reconstruct 1% low-dose PET scans. A 2D encoder-decoder network was implemented as the generator to synthesize a standard-dose image and a discriminator was used to evaluate them. The two networks contested with each other to achieve high visual quality PET from the ultra-low-dose PET. Multi-slice inputs were used to reduce noise by providing the network with 2.5D information. Feature matching was applied to reduce hallucinated structures. Task-specific perceptual loss was designed to maintain the correct pathological features. The image quality was evaluated by peak signal-to-noise ratio (PSNR), structural similarity (SSIM), and root mean square error (RMSE) metrics with and without each of these modules. Two expert radiologists were asked to score image quality on a five-point scale and identified the amyloid status (positive or negative).RESULTS: With only low-dose PET as input, the proposed method significantly outperformed Chen etal.'s method [9] (which shows the best performance in this task) with the same input (PET-only model) by 1.87 dB in PSNR, 2.04% in SSIM, and 24.75% in RMSE. It also achieved comparable results to Chen etal.'s method which used additional MRI inputs (PET-MR model). Experts' reading results showed that the proposed method could achieve better overall image quality and maintain better pathological features indicating amyloid status than both PET-only and PET-MR models proposed by Chen etal.CONCLUSION: Standard-dose amyloid PET images can be synthesized from ultra-low-dose images using GAN. Applying adversarial learning, feature matching, and task-specific perceptual loss are essential to ensure image quality and the preservation of pathological features. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1002/mp.13626

  View details for PubMedID 31131901

• An MRI Compatible RF MEMs Controlled Wireless Power Transfer System IEEE TRANSACTIONS ON MICROWAVE THEORY AND TECHNIQUES Byron, K., Winkler, S. A., Robb, F., Vasanawala, S., Pauly, J., Scott, G. 2019; 67 (5): 1717–26

  View details for DOI 10.1109/TMTT.2019.2902554

  View details for Web of Science ID 000467528800007

• An MRI Compatible RF MEMs Controlled Wireless Power Transfer System. IEEE transactions on microwave theory and techniques Byron, K., Winkler, S. A., Robb, F., Vasanawala, S., Pauly, J., Scott, G. 2019; 67 (5): 1717-1726

  Abstract

  In magnetic resonance imaging (MRI), wearable wireless receive coil arrays are a key technology goal. An MRI compatible wireless power transfer (WPT) system will be needed to realize this technology. An MRI WPT system must withstand the extreme electromagnetic environment of the scanner and cannot degrade MRI image quality. Here, a WPT system is developed for operation in MRI scanners using new microelectromechanical RF switch (RF MEMs) technology. The WPT system includes a class-E power amplifier, RF MEMs automated impedance matching, a primary coil array employing RF MEMs power steering, and a flexible secondary coil with class E rectification. To adapt WPT technology to MRI, techniques are developed for operation at high magnetic field, and to mitigate the RF interactions between the scanner and WPT system. A major challenge was the identification and suppression of noise and harmonic interference, by gating, filtering, and rectifier topologies. The system can achieve 63% efficiency while exceeding 13 W delivery over a coil distance of 3.5 cm. For continuous WPT beyond 5W, added filters and full-wave class E rectification lowers harmonic generation at some cost to efficiency, while image SNR reaches about 32% of the ideal. RF-gated WPT, which interrupts power transfer in the MRI signal acquisition interval, achieves SNR performance to within 1 dB of the ideal. With further refinement, the inclusion of WPT technology in MRI scanners appears completely feasible.

  View details for DOI 10.1109/TMTT.2019.2902554

  View details for PubMedID 31423023

  View details for PubMedCentralID PMC6696940

• Evaluation of a Flexible 12-Channel Screen-printed Pediatric MRI Coil RADIOLOGY Winkler, S., Corea, J., Lechene, B., O'Brien, K., Bonanni, J., Chauelhari, A., Alley, M., Taviani, V., Grafendorfer, T., Robb, F., Seem, G., Pauly, J., Lustig, M., Arias, A., Vasanawala, S. 2019; 291 (1): 179–84

  View details for DOI 10.1148/radiol.2019181883

  View details for Web of Science ID 000465222600036

• Evaluation of a Flexible 12-Channel Screen-printed Pediatric MRI Coil. Radiology Winkler, S. A., Corea, J., Lechene, B., O'Brien, K., Bonanni, J. R., Chaudhari, A., Alley, M., Taviani, V., Grafendorfer, T., Robb, F., Scott, G., Pauly, J., Lustig, M., Arias, A. C., Vasanawala, S. 2019: 181883

  Abstract

  Background Screen-printed MRI coil technology may reduce the need for bulky and heavy housing of coil electronics and may provide a better fit to patient anatomy to improve coil performance. Purpose To assess the performance and caregiver and clinician acceptance of a pediatric-sized screen-printed flexible MRI coil array as compared with conventional coil technology. Materials and Methods A pediatric-sized 12-channel coil array was designed by using a screen-printing process. Element coupling and phantom signal-to-noise ratio (SNR) were assessed. Subjects were scanned by using the pediatric printed array between September and November 2017; results were compared with three age- and sex-matched historical control subjects by using a commercial 32-channel cardiac array at 3 T. Caregiver acceptance was assessed by asking nurses, technologists, anesthesiologists, and subjects or parents to rate their coil preference. Diagnostic quality of the images was evaluated by using a Likert scale (5 = high image quality, 1 = nondiagnostic). Image SNR was evaluated and compared. Results Twenty study participants were evaluated with the screen-printed coil (age range, 2 days to 12 years; 11 male and nine female subjects). Loaded pediatric phantom testing yielded similar noise covariance matrices and only slightly degraded SNR for the printed coil as compared with the commercial coil. The caregiver acceptance survey yielded a mean score of 4.1 ± 0.6 (scale: 1, preferred the commercial coil; 5, preferred the printed coil). Diagnostic quality score was 4.5 ± 0.6. Mean image SNR was 54 ± 49 (paraspinal muscle), 78 ± 51 (abdominal wall muscle), and 59 ± 35 (psoas) for the printed coil, as compared with 64 ± 55, 65 ± 48, and 57 ± 43, respectively, for the commercial coil; these SNR differences were not statistically significant (P = .26). Conclusion A flexible screen-printed pediatric MRI receive coil yields adequate signal-to-noise ratio in phantoms and pediatric study participants, with similar image quality but higher preference by subjects and their caregivers when compared with a conventional MRI coil. © RSNA, 2019 Online supplemental material is available for this article. See also the editorial by Lamb in this issue.

  View details for PubMedID 30806599

• Data-driven self-calibration and reconstruction for non-cartesian wave-encoded single-shot fast spin echo using deep learning. Journal of magnetic resonance imaging : JMRI Chen, F. n., Cheng, J. Y., Taviani, V. n., Sheth, V. R., Brunsing, R. L., Pauly, J. M., Vasanawala, S. S. 2019

  Abstract

  Current self-calibration and reconstruction methods for wave-encoded single-shot fast spin echo imaging (SSFSE) requires long computational time, especially when high accuracy is needed.To develop and investigate the clinical feasibility of data-driven self-calibration and reconstruction of wave-encoded SSFSE imaging for computation time reduction and quality improvement.Prospective controlled clinical trial.With Institutional Review Board approval, the proposed method was assessed on 29 consecutive adult patients (18 males, 11 females, range, 24-77 years).A wave-encoded variable-density SSFSE sequence was developed for clinical 3.0T abdominal scans to enable 3.5× acceleration with full-Fourier acquisitions. Data-driven calibration of wave-encoding point-spread function (PSF) was developed using a trained deep neural network. Data-driven reconstruction was developed with another set of neural networks based on the calibrated wave-encoding PSF. Training of the calibration and reconstruction networks was performed on 15,783 2D wave-encoded SSFSE abdominal images.Image quality of the proposed data-driven approach was compared independently and blindly with a conventional approach using iterative self-calibration and reconstruction with parallel imaging and compressed sensing by three radiologists on a scale from -2 to 2 for noise, contrast, sharpness, artifacts, and confidence. Computation time of these two approaches was also compared.Wilcoxon signed-rank tests were used to compare image quality and two-tailed t-tests were used to compare computation time with P values of under 0.05 considered statistically significant.An average 2.1-fold speedup in computation was achieved using the proposed method. The proposed data-driven self-calibration and reconstruction approach significantly reduced the perceived noise level (mean scores 0.82, P < 0.0001).The proposed data-driven calibration and reconstruction achieved twice faster computation with reduced perceived noise, providing a fast and robust self-calibration and reconstruction for clinical abdominal SSFSE imaging.1 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019.

  View details for DOI 10.1002/jmri.26871

  View details for PubMedID 31322799

• Thermo-acoustic ultrasound for noninvasive temperature monitoring at lead tips during MRI. Magnetic resonance in medicine Dixit, N. n., Pauly, J. M., Scott, G. C. 2019

  Abstract

  We explore the use of thermo-acoustic ultrasound (TAUS) to monitor temperature at the tips of conductive device leads during MRI.In TAUS, rapid radiofrequency (RF) power deposition excites an acoustic signal via thermoelastic expansion. Coupling of the MRI RF transmit to device leads causes SAR amplification at lead tips, allowing MRI RF transmitters to excite significant lead tip TAUS signals. Because the amplitude of the TAUS signal depends on temperature, it becomes feasible to monitor the lead tip temperature during MRI by tracking the TAUS amplitude.The TAUS temperature dependence was characterized in a phantom and in tissue. To perform TAUS acquisitions in an MRI scanner, amplitude modulated RF chirps were transmitted by the body coil, and the lead tip TAUS signal was detected by an ultrasonic transducer. The TAUS signal level was correlated with the RF current induced on the lead and the associated B 1 artifacts in MRI. TAUS signals acquired during RF-induced heating were used to estimate the lead tip temperature.The TAUS signal exhibited strong dependence on temperature, increasing over 30% with 10 ∘ C of heating both in the phantom and in tissue. A lead tip TAUS signal was observed for a 100 mA rms current induced on a lead. During RF-induced heating, the TAUS signal appeared to accurately approximate the peak lead tip temperature.TAUS allows for noninvasive monitoring of lead tip temperature in an MRI environment. With further development, TAUS opens new avenues to improve RF device safety during MRI scans.

  View details for DOI 10.1002/mrm.28152

  View details for PubMedID 31883207

• Task-GAN: Improving Generative Adversarial Network for Image Reconstruction Ouyang, J., Wang, G., Gong, E., Chen, K., Pauly, J., Zaharchuk, G., Knoll, F., Maier, A., Rueckert, D., Ye, J. C. SPRINGER INTERNATIONAL PUBLISHING AG. 2019: 193–204

  View details for DOI 10.1007/978-3-030-33843-5_18

  View details for Web of Science ID 000582481700018

• Accelerated MRI Reconstruction with Dual-Domain Generative Adversarial Network Wang, G., Gong, E., Banerjee, S., Pauly, J., Zaharchuk, G., Knoll, F., Maier, A., Rueckert, D., Ye, J. C. SPRINGER INTERNATIONAL PUBLISHING AG. 2019: 47–57

  View details for DOI 10.1007/978-3-030-33843-5_5

  View details for Web of Science ID 000582481700005

• Deep Generative Adversarial Neural Networks for Compressive Sensing MRI IEEE TRANSACTIONS ON MEDICAL IMAGING Mardani, M., Gong, E., Cheng, J. Y., Vasanawala, S. S., Zaharchuk, G., Xing, L., Pauly, J. M. 2019; 38 (1): 167–79

  Abstract

  Undersampled magnetic resonance image (MRI) reconstruction is typically an ill-posed linear inverse task. The time and resource intensive computations require tradeoffs between accuracy and speed. In addition, state-of-the-art compressed sensing (CS) analytics are not cognizant of the image diagnostic quality. To address these challenges, we propose a novel CS framework that uses generative adversarial networks (GAN) to model the (low-dimensional) manifold of high-quality MR images. Leveraging a mixture of least-squares (LS) GANs and pixel-wise l1/l2 cost, a deep residual network with skip connections is trained as the generator that learns to remove the aliasing artifacts by projecting onto the image manifold. The LSGAN learns the texture details, while the l1/l2 cost suppresses high-frequency noise. A discriminator network, which is a multilayer convolutional neural network (CNN), plays the role of a perceptual cost that is then jointly trained based on high-quality MR images to score the quality of retrieved images. In the operational phase, an initial aliased estimate (e.g., simply obtained by zero-filling) is propagated into the trained generator to output the desired reconstruction. This demands a very low computational overhead. Extensive evaluations are performed on a large contrast-enhanced MR dataset of pediatric patients. Images rated by expert radiologists corroborate that GANCS retrieves higher quality images with improved fine texture details compared with conventional Wavelet-based and dictionary-learning-based CS schemes as well as with deep-learning-based schemes using pixel-wise training. In addition, it offers reconstruction times of under a few milliseconds, which are two orders of magnitude faster than the current state-of-the-art CS-MRI schemes.

  View details for DOI 10.1109/TMI.2018.2858752

  View details for Web of Science ID 000455110500017

  View details for PubMedID 30040634

• Automatically Determining the Confocal Parameters From OCT B-Scans for Quantification of the Attenuation Coefficients IEEE TRANSACTIONS ON MEDICAL IMAGING Dwork, N., Smith, G. T., Leng, T., Pauly, J. M., Bowden, A. K. 2019; 38 (1): 261–68

  Abstract

  The attenuation coefficient is a relevant biomarker for many diagnostic medical applications. Recently, the Depth-Resolved Confocal (DRC) technique was developed to automatically estimate the attenuation coefficients from Optical Coherence Tomography (OCT) data with pixel-level resolution. However, DRC requires that the confocal function parameters (i.e., focal plane location and apparent Rayleigh range) be known a priori. In this paper, we present the autoConfocal algorithm: a simple, automatic method for estimating those parameters directly from OCT imagery when the focal plane is within the sample. We present autoConfocal+DRC results on phantom data, ex-vivo biological tissue data, and in-vivo clinical data.

  View details for DOI 10.1109/TMI.2018.2861570

  View details for Web of Science ID 000455110500025

  View details for PubMedID 30072317

• Deep residual network for off-resonance artifact correction with application to pediatric body MRA with 3D cones. Magnetic resonance in medicine Zeng, D. Y., Shaikh, J. n., Holmes, S. n., Brunsing, R. L., Pauly, J. M., Nishimura, D. G., Vasanawala, S. S., Cheng, J. Y. 2019

  Abstract

  To enable rapid imaging with a scan time-efficient 3D cones trajectory with a deep-learning off-resonance artifact correction technique.A residual convolutional neural network to correct off-resonance artifacts (Off-ResNet) was trained with a prospective study of pediatric MRA exams. Each exam acquired a short readout scan (1.18 ms ± 0.38) and a long readout scan (3.35 ms ± 0.74) at 3 T. Short readout scans, with longer scan times but negligible off-resonance blurring, were used as reference images and augmented with additional off-resonance for supervised training examples. Long readout scans, with greater off-resonance artifacts but shorter scan time, were corrected by autofocus and Off-ResNet and compared with short readout scans by normalized RMS error, structural similarity index, and peak SNR. Scans were also compared by scoring on 8 anatomical features by two radiologists, using analysis of variance with post hoc Tukey's test and two one-sided t-tests. Reader agreement was determined with intraclass correlation.The total scan time for long readout scans was on average 59.3% shorter than short readout scans. Images from Off-ResNet had superior normalized RMS error, structural similarity index, and peak SNR compared with uncorrected images across ±1 kHz off-resonance (P < .01). The proposed method had superior normalized RMS error over -677 Hz to +1 kHz and superior structural similarity index and peak SNR over ±1 kHz compared with autofocus (P < .01). Radiologic scoring demonstrated that long readout scans corrected with Off-ResNet were noninferior to short readout scans (P < .05).The proposed method can correct off-resonance artifacts from rapid long-readout 3D cones scans to a noninferior image quality compared with diagnostically standard short readout scans.

  View details for DOI 10.1002/mrm.27825

  View details for PubMedID 31115936

• Ultra-Low-Dose 18F-Florbetaben Amyloid PET Imaging Using Deep Learning with Multi-Contrast MRI Inputs. Radiology Chen, K. T., Gong, E., de Carvalho Macruz, F. B., Xu, J., Boumis, A., Khalighi, M., Poston, K. L., Sha, S. J., Greicius, M. D., Mormino, E., Pauly, J. M., Srinivas, S., Zaharchuk, G. 2018: 180940

  Abstract

  Purpose To reduce radiotracer requirements for amyloid PET/MRI without sacrificing diagnostic quality by using deep learning methods. Materials and Methods Forty data sets from 39 patients (mean age ± standard deviation [SD], 67 years ± 8), including 16 male patients and 23 female patients (mean age, 66 years ± 6 and 68 years ± 9, respectively), who underwent simultaneous amyloid (fluorine 18 [18F]-florbetaben) PET/MRI examinations were acquired from March 2016 through October 2017 and retrospectively analyzed. One hundredth of the raw list-mode PET data were randomly chosen to simulate a low-dose (1%) acquisition. Convolutional neural networks were implemented with low-dose PET and multiple MR images (PET-plus-MR model) or with low-dose PET alone (PET-only) as inputs to predict full-dose PET images. Quality of the synthesized images was evaluated while Bland-Altman plots assessed the agreement of regional standard uptake value ratios (SUVRs) between image types. Two readers scored image quality on a five-point scale (5 = excellent) and determined amyloid status (positive or negative). Statistical analyses were carried out to assess the difference of image quality metrics and reader agreement and to determine confidence intervals (CIs) for reading results. Results The synthesized images (especially from the PET-plus-MR model) showed marked improvement on all quality metrics compared with the low-dose image. All PET-plus-MR images scored 3 or higher, with proportions of images rated greater than 3 similar to those for the full-dose images (-10% difference [eight of 80 readings], 95% CI: -15%, -5%). Accuracy for amyloid status was high (71 of 80 readings [89%]) and similar to intrareader reproducibility of full-dose images (73 of 80 [91%]). The PET-plus-MR model also had the smallest mean and variance for SUVR difference to full-dose images. Conclusion Simultaneously acquired MRI and ultra-low-dose PET data can be used to synthesize full-dose-like amyloid PET images. © RSNA, 2018 Online supplemental material is available for this article.

  View details for PubMedID 30526350

• Hyperpolarized 13C MRI: Path to Clinical Translation in Oncology. Neoplasia (New York, N.Y.) Kurhanewicz, J., Vigneron, D. B., Ardenkjaer-Larsen, J. H., Bankson, J. A., Brindle, K., Cunningham, C. H., Gallagher, F. A., Keshari, K. R., Kjaer, A., Laustsen, C., Mankoff, D. A., Merritt, M. E., Nelson, S. J., Pauly, J. M., Lee, P., Ronen, S., Tyler, D. J., Rajan, S. S., Spielman, D. M., Wald, L., Zhang, X., Malloy, C. R., Rizi, R. 2018; 21 (1): 1–16

  Abstract

  This white paper discusses prospects for advancing hyperpolarization technology to better understand cancer metabolism, identify current obstacles to HP (hyperpolarized) 13C magnetic resonance imaging's (MRI's) widespread clinical use, and provide recommendations for overcoming them. Since the publication of the first NIH white paper on hyperpolarized 13C MRI in 2011, preclinical studies involving [1-13C]pyruvate as well a number of other 13C labeled metabolic substrates have demonstrated this technology's capacity to provide unique metabolic information. A dose-ranging study of HP [1-13C]pyruvate in patients with prostate cancer established safety and feasibility of this technique. Additional studies are ongoing in prostate, brain, breast, liver, cervical, and ovarian cancer. Technology for generating and delivering hyperpolarized agents has evolved, and new MR data acquisition sequences and improved MRI hardware have been developed. It will be important to continue investigation and development of existing and new probes in animal models. Improved polarization technology, efficient radiofrequency coils, and reliable pulse sequences are all important objectives to enable exploration of the technology in healthy control subjects and patient populations. It will be critical to determine how HP 13C MRI might fill existing needs in current clinical research and practice, and complement existing metabolic imaging modalities. Financial sponsorship and integration of academia, industry, and government efforts will be important factors in translating the technology for clinical research in oncology. This white paper is intended to provide recommendations with this goal in mind.

  View details for PubMedID 30472500

• Technique development of 3D dynamic CS-EPSI for hyperpolarized C-13 pyruvate MR molecular imaging of human prostate cancer MAGNETIC RESONANCE IN MEDICINE Chen, H., Larson, P. Z., Gordon, J. W., Bok, R. A., Ferrone, M., van Criekinge, M., Carvajal, L., Cao, P., Pauly, J. M., Kerr, A. B., Park, I., Slater, J. B., Nelson, S. J., Munster, P. N., Aggarwal, R., Kurhanewicz, J., Vigneron, D. B. 2018; 80 (5): 2062–72

  Abstract

  The purpose of this study was to develop a new 3D dynamic carbon-13 compressed sensing echoplanar spectroscopic imaging (EPSI) MR sequence and test it in phantoms, animal models, and then in prostate cancer patients to image the metabolic conversion of hyperpolarized [1-13 C]pyruvate to [1-13 C]lactate with whole gland coverage at high spatial and temporal resolution.A 3D dynamic compressed sensing (CS)-EPSI sequence with spectral-spatial excitation was designed to meet the required spatial coverage, time and spatial resolution, and RF limitations of the 3T MR scanner for its clinical translation for prostate cancer patient imaging. After phantom testing, animal studies were performed in rats and transgenic mice with prostate cancers. For patient studies, a GE SPINlab polarizer (GE Healthcare, Waukesha, WI) was used to produce hyperpolarized sterile GMP [1-13 C]pyruvate. 3D dynamic 13 C CS-EPSI data were acquired starting 5 s after injection throughout the gland with a spatial resolution of 0.5 cm3 , 18 time frames, 2-s temporal resolution, and 36 s total acquisition time.Through preclinical testing, the 3D CS-EPSI sequence developed in this project was shown to provide the desired spectral, temporal, and spatial 5D HP 13 C MR data. In human studies, the 3D dynamic HP CS-EPSI approach provided first-ever simultaneously volumetric and dynamic images of the LDH-catalyzed conversion of [1-13 C]pyruvate to [1-13 C]lactate in a biopsy-proven prostate cancer patient with full gland coverage.The results demonstrate the feasibility to characterize prostate cancer metabolism in animals, and now patients using this new 3D dynamic HP MR technique to measure kPL , the kinetic rate constant of [1-13 C]pyruvate to [1-13 C]lactate conversion.

  View details for PubMedID 29575178

  View details for PubMedCentralID PMC6107425

• Variable-Density Single-Shot Fast Spin-Echo MRI with Deep Learning Reconstruction by Using Variational Networks RADIOLOGY Chen, F., Taviani, V., Malkiel, I., Cheng, J. Y., Tamir, J. I., Shaikh, J., Chang, S. T., Hardy, C. J., Pauly, J. M., Vasanawala, S. S. 2018; 289 (2): 366–73

  View details for DOI 10.1148/radiol.2018180445

  View details for Web of Science ID 000447652300015

• Quantitative susceptibility mapping using deep neural network: QSMnet NEUROIMAGE Yoon, J., Gong, E., Chatnuntawech, I., Bilgic, B., Lee, J., Jung, W., Ko, J., Jung, H., Setsompop, K., Zaharchuk, G., Kim, E., Pauly, J., Lee, J. 2018; 179: 199–206

  Abstract

  Deep neural networks have demonstrated promising potential for the field of medical image reconstruction, successfully generating high quality images for CT, PET and MRI. In this work, an MRI reconstruction algorithm, which is referred to as quantitative susceptibility mapping (QSM), has been developed using a deep neural network in order to perform dipole deconvolution, which restores magnetic susceptibility source from an MRI field map. Previous approaches of QSM require multiple orientation data (e.g. Calculation of Susceptibility through Multiple Orientation Sampling or COSMOS) or regularization terms (e.g. Truncated K-space Division or TKD; Morphology Enabled Dipole Inversion or MEDI) to solve an ill-conditioned dipole deconvolution problem. Unfortunately, they either entail challenges in data acquisition (i.e. long scan time and multiple head orientations) or suffer from image artifacts. To overcome these shortcomings, a deep neural network, which is referred to as QSMnet, is constructed to generate a high quality susceptibility source map from single orientation data. The network has a modified U-net structure and is trained using COSMOS QSM maps, which are considered as gold standard. Five head orientation datasets from five subjects were employed for patch-wise network training after doubling the training data using a model-based data augmentation. Seven additional datasets of five head orientation images (i.e. total 35 images) were used for validation (one dataset) and test (six datasets). The QSMnet maps of the test dataset were compared with the maps from TKD and MEDI for their image quality and consistency with respect to multiple head orientations. Quantitative and qualitative image quality comparisons demonstrate that the QSMnet results have superior image quality to those of TKD or MEDI results and have comparable image quality to those of COSMOS. Additionally, QSMnet maps reveal substantially better consistency across the multiple head orientation data than those from TKD or MEDI. As a preliminary application, the network was further tested for three patients, one with microbleed, another with multiple sclerosis lesions, and the third with hemorrhage. The QSMnet maps showed similar lesion contrasts with those from MEDI, demonstrating potential for future applications.

  View details for PubMedID 29894829

• ISLES 2016 and 2017-Benchmarking Ischemic Stroke Lesion Outcome Prediction Based on Multispectral MRI FRONTIERS IN NEUROLOGY Winzeck, S., Hakim, A., McKinley, R., Pinto, J. R., Alves, V., Silva, C., Pisov, M., Krivov, E., Belyaev, M., Monteiro, M., Oliveira, A., Choi, Y., Palk, M., Kwon, Y., Lee, H., Kim, B., Won, J., Islam, M., Ren, H., Robben, D., Suetens, P., Gong, E., Niu, Y., Xu, J., Pauly, J. M., Lucas, C., Heinrich, M. P., Rivera', L. C., Castillo, L. S., Daza, L. A., Beers, A. L., Arbelaers, P., Maier, O., Chang, K., Brown, J. M., Kapalthy-Cramer, J., Zaharchuk, G., Wiest, R., Reyes, M. 2018; 9

  View details for DOI 10.3389/fneur.2018.00679

  View details for Web of Science ID 000444461500001

• ISLES 2016 and 2017-Benchmarking Ischemic Stroke Lesion Outcome Prediction Based on Multispectral MRI. Frontiers in neurology Winzeck, S., Hakim, A., McKinley, R., Pinto, J. A., Alves, V., Silva, C., Pisov, M., Krivov, E., Belyaev, M., Monteiro, M., Oliveira, A., Choi, Y., Paik, M. C., Kwon, Y., Lee, H., Kim, B. J., Won, J. H., Islam, M., Ren, H., Robben, D., Suetens, P., Gong, E., Niu, Y., Xu, J., Pauly, J. M., Lucas, C., Heinrich, M. P., Rivera, L. C., Castillo, L. S., Daza, L. A., Beers, A. L., Arbelaezs, P., Maier, O., Chang, K., Brown, J. M., Kalpathy-Cramer, J., Zaharchuk, G., Wiest, R., Reyes, M. 2018; 9: 679

  Abstract

  Performance of models highly depend not only on the used algorithm but also the data set it was applied to. This makes the comparison of newly developed tools to previously published approaches difficult. Either researchers need to implement others' algorithms first, to establish an adequate benchmark on their data, or a direct comparison of new and old techniques is infeasible. The Ischemic Stroke Lesion Segmentation (ISLES) challenge, which has ran now consecutively for 3 years, aims to address this problem of comparability. ISLES 2016 and 2017 focused on lesion outcome prediction after ischemic stroke: By providing a uniformly pre-processed data set, researchers from all over the world could apply their algorithm directly. A total of nine teams participated in ISLES 2015, and 15 teams participated in ISLES 2016. Their performance was evaluated in a fair and transparent way to identify the state-of-the-art among all submissions. Top ranked teams almost always employed deep learning tools, which were predominately convolutional neural networks (CNNs). Despite the great efforts, lesion outcome prediction persists challenging. The annotated data set remains publicly available and new approaches can be compared directly via the online evaluation system, serving as a continuing benchmark (www.isles-challenge.org).

  View details for DOI 10.3389/fneur.2018.00679

  View details for PubMedID 30271370

  View details for PubMedCentralID PMC6146088

• Variable-Density Single-Shot Fast Spin-Echo MRI with Deep Learning Reconstruction by Using Variational Networks. Radiology Chen, F., Taviani, V., Malkiel, I., Cheng, J. Y., Tamir, J. I., Shaikh, J., Chang, S. T., Hardy, C. J., Pauly, J. M., Vasanawala, S. S. 2018: 180445

  Abstract

  Purpose To develop a deep learning reconstruction approach to improve the reconstruction speed and quality of highly undersampled variable-density single-shot fast spin-echo imaging by using a variational network (VN), and to clinically evaluate the feasibility of this approach. Materials and Methods Imaging was performed with a 3.0-T imager with a coronal variable-density single-shot fast spin-echo sequence at 3.25 times acceleration in 157 patients referred for abdominal imaging (mean age, 11 years; range, 1-34 years; 72 males [mean age, 10 years; range, 1-26 years] and 85 females [mean age, 12 years; range, 1-34 years]) between March 2016 and April 2017. A VN was trained based on the parallel imaging and compressed sensing (PICS) reconstruction of 130 patients. The remaining 27 patients were used for evaluation. Image quality was evaluated in an independent blinded fashion by three radiologists in terms of overall image quality, perceived signal-to-noise ratio, image contrast, sharpness, and residual artifacts with scores ranging from 1 (nondiagnostic) to 5 (excellent). Wilcoxon tests were performed to test the hypothesis that there was no significant difference between VN and PICS. Results VN achieved improved perceived signal-to-noise ratio (P = .01) and improved sharpness (P < .001), with no difference in image contrast (P = .24) and residual artifacts (P = .07). In terms of overall image quality, VN performed better than did PICS (P = .02). Average reconstruction time ± standard deviation was 5.60 seconds ± 1.30 per section for PICS and 0.19 second ± 0.04 per section for VN. Conclusion Compared with the conventional parallel imaging and compressed sensing reconstruction (PICS), the variational network (VN) approach accelerates the reconstruction of variable-density single-shot fast spin-echo sequences and achieves improved overall image quality with higher perceived signal-to-noise ratio and sharpness.

  View details for PubMedID 30040039

• Body diffusion-weighted imaging using magnetization prepared single-shot fast spin echo and extended parallel imaging signal averaging MAGNETIC RESONANCE IN MEDICINE Gibbons, E. K., Vasanawala, S. S., Pauly, J. M., Kerr, A. B. 2018; 79 (6): 3032–44

  Abstract

  This work demonstrates a magnetization prepared diffusion-weighted single-shot fast spin echo (SS-FSE) pulse sequence for the application of body imaging to improve robustness to geometric distortion. This work also proposes a scan averaging technique that is superior to magnitude averaging and is not subject to artifacts due to object phase.This single-shot sequence is robust against violation of the Carr-Purcell-Meiboom-Gill (CPMG) condition. This is achieved by dephasing the signal after diffusion weighting and tipping the MG component of the signal onto the longitudinal axis while the non-MG component is spoiled. The MG signal component is then excited and captured using a traditional SS-FSE sequence, although the echo needs to be recalled prior to each echo. Extended Parallel Imaging (ExtPI) averaging is used where coil sensitivities from the multiple acquisitions are concatenated into one large parallel imaging (PI) problem. The size of the PI problem is reduced by SVD-based coil compression which also provides background noise suppression. This sequence and reconstruction are evaluated in simulation, phantom scans, and in vivo abdominal clinical cases.Simulations show that the sequence generates a stable signal throughout the echo train which leads to good image quality. This sequence is inherently low-SNR, but much of the SNR can be regained through scan averaging and the proposed ExtPI reconstruction. In vivo results show that the proposed method is able to provide diffusion encoded images while mitigating geometric distortion artifacts compared to EPI.This work presents a diffusion-prepared SS-FSE sequence that is robust against the violation of the CPMG condition while providing diffusion contrast in clinical cases. Magn Reson Med 79:3032-3044, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

  View details for PubMedID 29044721

• Rapid compressed sensing reconstruction of 3D non-Cartesian MRI MAGNETIC RESONANCE IN MEDICINE Baron, C. A., Dwork, N., Pauly, J. M., Nishimura, D. G. 2018; 79 (5): 2685–92

  Abstract

  Conventional non-Cartesian compressed sensing requires multiple nonuniform Fourier transforms every iteration, which is computationally expensive. Accordingly, time-consuming reconstructions have slowed the adoption of undersampled 3D non-Cartesian acquisitions into clinical protocols. In this work we investigate several approaches to minimize reconstruction times without sacrificing accuracy.The reconstruction problem can be reformatted to exploit the Toeplitz structure of matrices that are evaluated every iteration, but it requires larger oversampling than what is strictly required by nonuniform Fourier transforms. Accordingly, we investigate relative speeds of the two approaches for various nonuniform Fourier transform kernel sizes and oversampling for both GPU and CPU implementations. Second, we introduce a method to minimize matrix sizes by estimating the image support. Finally, density compensation weights have been used as a preconditioning matrix to improve convergence, but this increases noise. We propose a more general approach to preconditioning that allows a trade-off between accuracy and convergence speed.When using a GPU, the Toeplitz approach was faster for all practical parameters. Second, it was found that properly accounting for image support can prevent aliasing errors with minimal impact on reconstruction time. Third, the proposed preconditioning scheme improved convergence rates by an order of magnitude with negligible impact on noise.With the proposed methods, 3D non-Cartesian compressed sensing with clinically relevant reconstruction times (<2 min) is feasible using practical computer resources. Magn Reson Med 79:2685-2692, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

  View details for PubMedID 28940748

• Deep learning enables reduced gadolinium dose for contrast-enhanced brain MRI. Journal of magnetic resonance imaging : JMRI Gong, E., Pauly, J. M., Wintermark, M., Zaharchuk, G. 2018

  Abstract

  BACKGROUND: There are concerns over gadolinium deposition from gadolinium-based contrast agents (GBCA) administration.PURPOSE: To reduce gadolinium dose in contrast-enhanced brain MRI using a deep learning method.STUDY TYPE: Retrospective, crossover.POPULATION: Sixty patients receiving clinically indicated contrast-enhanced brain MRI.SEQUENCE: 3D T1 -weighted inversion-recovery prepped fast-spoiled-gradient-echo (IR-FSPGR) imaging was acquired at both 1.5T and 3T. In 60 brain MRI exams, the IR-FSPGR sequence was obtained under three conditions: precontrast, postcontrast images with 10% low-dose (0.01mmol/kg) and 100% full-dose (0.1 mmol/kg) of gadobenate dimeglumine. We trained a deep learning model using the first 10 cases (with mixed indications) to approximate full-dose images from the precontrast and low-dose images. Synthesized full-dose images were created using the trained model in two test sets: 20 patients with mixed indications and 30 patients with glioma.ASSESSMENT: For both test sets, low-dose, true full-dose, and the synthesized full-dose postcontrast image sets were compared quantitatively using peak-signal-to-noise-ratios (PSNR) and structural-similarity-index (SSIM). For the test set comprised of 20 patients with mixed indications, two neuroradiologists scored blindly and independently for the three postcontrast image sets, evaluating image quality, motion-artifact suppression, and contrast enhancement compared with precontrast images.STATISTICAL ANALYSIS: Results were assessed using paired t-tests and noninferiority tests.RESULTS: The proposed deep learning method yielded significant (n=50, P<0.001) improvements over the low-dose images (>5 dB PSNR gains and >11.0% SSIM). Ratings on image quality (n=20, P=0.003) and contrast enhancement (n=20, P<0.001) were significantly increased. Compared to true full-dose images, the synthesized full-dose images have a slight but not significant reduction in image quality (n=20, P=0.083) and contrast enhancement (n=20, P=0.068). Slightly better (n=20, P=0.039) motion-artifact suppression was noted in the synthesized images. The noninferiority test rejects the inferiority of the synthesized to true full-dose images for image quality (95% CI: -14-9%), artifacts suppression (95% CI: -5-20%), and contrast enhancement (95% CI: -13-6%).DATA CONCLUSION: With the proposed deep learning method, gadolinium dose can be reduced 10-fold while preserving contrast information and avoiding significant image quality degradation.LEVEL OF EVIDENCE: 3 Technical Efficacy: Stage 5 J. Magn. Reson. Imaging 2018.

  View details for PubMedID 29437269

• Thermo-Acoustic Ultrasound for Detection of RF-Induced Device Lead Heating in MRI IEEE TRANSACTIONS ON MEDICAL IMAGING Dixit, N., Stang, P. P., Pauly, J. M., Scott, G. C. 2018; 37 (2): 536–46

  Abstract

  Patients who have implanted medical devices with long conductive leads are often restricted from receiving MRI scans due to the danger of RF-induced heating near the lead tips. Phantom studies have shown that this heating varies significantly on a case-by-case basis, indicating that many patients with implanted devices can receive clinically useful MRI scans without harm. However, the difficulty of predicting RF-induced lead tip heating prior to scanning prevents numerous implant recipients from being scanned. Here, we demonstrate that thermo-acoustic ultrasound (TAUS) has the potential to be utilized for a pre-scan procedure assessing the risk of RF-induced lead tip heating in MRI. A system was developed to detect TAUS signals by four different TAUS acquisition methods. We then integrated this system with an MRI scanner and detected a peak in RF power absorption near the tip of a model lead when transmitting from the scanner's body coil. We also developed and experimentally validated simulations to characterize the thermo-acoustic signal generated near lead tips. These results indicate that TAUS is a promising method for assessing RF implant safety, and with further development, a TAUS pre-scan could allow many more patients to have access to MRI scans of significant clinical value.

  View details for DOI 10.1109/TMI.2017.2764425

  View details for Web of Science ID 000424467000019

  View details for PubMedID 29053449

  View details for PubMedCentralID PMC5942199

• Self-Calibrating Wave-Encoded Variable-Density Single-Shot Fast Spin Echo Imaging. Journal of magnetic resonance imaging : JMRI Chen, F. n., Taviani, V. n., Tamir, J. I., Cheng, J. Y., Zhang, T. n., Song, Q. n., Hargreaves, B. A., Pauly, J. M., Vasanawala, S. S. 2018; 47 (4): 954–66

  Abstract

  It is highly desirable in clinical abdominal MR scans to accelerate single-shot fast spin echo (SSFSE) imaging and reduce blurring due to T2 decay and partial-Fourier acquisition.To develop and investigate the clinical feasibility of wave-encoded variable-density SSFSE imaging for improved image quality and scan time reduction.Prospective controlled clinical trial.With Institutional Review Board approval and informed consent, the proposed method was assessed on 20 consecutive adult patients (10 male, 10 female, range, 24-84 years).A wave-encoded variable-density SSFSE sequence was developed for clinical 3.0T abdominal scans to enable high acceleration (3.5×) with full-Fourier acquisitions by: 1) introducing wave encoding with self-refocusing gradient waveforms to improve acquisition efficiency; 2) developing self-calibrated estimation of wave-encoding point-spread function and coil sensitivity to improve motion robustness; and 3) incorporating a parallel imaging and compressed sensing reconstruction to reconstruct highly accelerated datasets.Image quality was compared pairwise with standard Cartesian acquisition independently and blindly by two radiologists on a scale from -2 to 2 for noise, contrast, confidence, sharpness, and artifacts. The average ratio of scan time between these two approaches was also compared.A Wilcoxon signed-rank tests with a P value under 0.05 considered statistically significant.Wave-encoded variable-density SSFSE significantly reduced the perceived noise level and improved the sharpness of the abdominal wall and the kidneys compared with standard acquisition (mean scores 0.8, 1.2, and 0.8, respectively, P < 0.003). No significant difference was observed in relation to other features (P = 0.11). An average of 21% decrease in scan time was achieved using the proposed method.Wave-encoded variable-density sampling SSFSE achieves improved image quality with clinically relevant echo time and reduced scan time, thus providing a fast and robust approach for clinical SSFSE imaging.1 Technical Efficacy: Stage 6 J. Magn. Reson. Imaging 2018;47:954-966.

  View details for PubMedID 28906567

• A Wireless Power Transfer System for MRI Scanners Byron, K., Robb, F., Vasanawala, S., Pauly, J., Scott, G., IEEE IEEE. 2018

  View details for Web of Science ID 000462702400012

• Neural Proximal Gradient Descent for Compressive Imaging Mardani, M., Sun, Q., Vasawanala, S., Papyan, V., Monajemi, H., Pauly, J., Donoho, D., Bengio, S., Wallach, H., Larochelle, H., Grauman, K., CesaBianchi, N., Garnett, R. NEURAL INFORMATION PROCESSING SYSTEMS (NIPS). 2018

  View details for Web of Science ID 000461852004016

• Advancements in Low-cost, Long Endurance, Altitude Controlled Latex Balloons (ValBal) Sushko, A., Tedjarati, A., Creus-Costa, J., Marshland, K., Brown, P., Regland, D., Dean, J., Maldonado, S., Pauly, J. M., IEEE IEEE. 2018

  View details for Web of Science ID 000474397402022

• Robust Self-Carlibrating nCPMG Acquisition: Application to Body Diffusion-Weighted Imaging IEEE TRANSACTIONS ON MEDICAL IMAGING Gibbons, E. K., Le Roux, P., Vasanawala, S. S., Pauly, J. M., Kerr, A. B. 2018; 37 (1): 200–209

  Abstract

  This paper demonstrates a robust diffusion-weighted single-shot fast spin echo (SS-FSE) sequence in the presence of significant off-resonance, which includes a variable-density acquisition and a self-calibrated reconstruction as improvements. A non-Carr-Purcell-Meiboom-Gill (nCPMG) SS-FSE acquisition stabilizes both the main and parasitic echo families for each echo. This preserves both the in-phase and quadrature components of the magnetization throughout the echo train. However, nCPMG SS-FSE also promotes aliasing of the quadrature component, which complicates reconstruction. A new acquisition and reconstruction approach is presented here, where the field-of-view is effectively doubled, but a partial k-space and variable density sampling is used to improve scan efficiency. The technique is presented in phantom scans to validate SNR and robustness against rapidly varying object phase. In vivo healthy volunteer examples and the clinical cases are demonstrated in abdominal imaging. This new approach provides comparable SNR to previous nCPMG acquisition techniques as well as providing more uniform apparent diffusion coefficient maps in phantom scans. In vivo scans suggest that this method is more robust against motion than previous approaches. The proposed reconstruction is an improvement to the nCPMG sequence as it is auto-calibrating and is justified to accurately treat the signal model for the nCPMG SS-FSE sequence.

  View details for DOI 10.1109/TMI.2017.2741421

  View details for Web of Science ID 000419346900018

  View details for PubMedID 28829307

  View details for PubMedCentralID PMC5784776

• An RF-gated wireless power transfer system for wireless MRI receive arrays CONCEPTS IN MAGNETIC RESONANCE PART B-MAGNETIC RESONANCE ENGINEERING Byron, K., Robb, F., Stang, P., Vasanawala, S., Pauly, J., Scott, G. 2017; 47B (4)

  View details for DOI 10.1002/cmr.b.21360

  View details for Web of Science ID 000435269700001

• Frequency shifting reduces but does not eliminate acoustic interference between echolocating bats: A theoretical analysis. The Journal of the Acoustical Society of America Perkins, M. L., Frank, H. K., Pauly, J. M., Hadly, E. A. 2017; 142 (4): 2133

  Abstract

  Bats have been observed to shift the frequency of their echolocation calls in the presence of other echolocating bats, ostensibly as a way to reduce acoustic interference. Few studies, however, have examined the theoretical efficacy of such jamming avoidance responses. The present study uses the wideband ambiguity function to analyze the effects of acoustic interference from conspecifics and congeneric heterospecifics on the target acquisition ability of Myotis californicus and Myotis yumanensis, specifically whether unilateral or bilateral frequency shifts reduce the effects of such interference. Model results suggest that in conspecific interactions, M. yumanensis recovers its target acquisition ability more completely and with less absolute frequency shift than does M. californicus, but that alternative methods of jamming avoidance may be easier to implement. The optimal strategy for reducing heterospecific interference is for M. californicus to downshift its call and M. yumanensis to upshift its call, which exaggerates a preexisting difference in mean frequency between the calls of the two species. Further empirical research would elucidate whether these species do in practice actively employ frequency shifting or other means for jamming avoidance, as well as illuminate the role of acoustic interference in niche partitioning.

  View details for DOI 10.1121/1.5006928

  View details for PubMedID 29092549

• An RF-gated wireless power transfer system for wireless MRI receive arrays. Concepts in magnetic resonance. Part B, Magnetic resonance engineering Byron, K., Robb, F., Stang, P., Vasanawala, S., Pauly, J., Scott, G. 2017; 47B (4)

  Abstract

  In MRI systems, cable-free receive arrays would simplify setup while reducing the bulk and weight of coil arrays and improve patient comfort and throughput. Since battery power would limit scan time, wireless power transfer (WPT) is a viable option to continuously supply several watts of power to on-coil electronics. To minimize added noise and decouple the wireless power system from MRI coils, restrictions are placed on the coil geometry of the wireless power system, which are shown to limit its efficiency. Continuous power harvesting can also cause a large increase in the background noise of the image due to diode rectifier up-conversion of noise around the frequency of the transmitted power. However, by RF gating the transmitted power off during the MRI receive time while continuing to supply power from a storage capacitor, WPT is demonstrated to have minimal impact on image quality at received power levels up to 11 W. The integration of WPT with a 1.5T scanner is demonstrated.

  View details for DOI 10.1002/cmr.b.21360

  View details for PubMedID 31057343

  View details for PubMedCentralID PMC6498852

• Comprehensive Multi-Dimensional MRI for the Simultaneous Assessment of Cardiopulmonary Anatomy and Physiology. Scientific reports Cheng, J. Y., Zhang, T., Alley, M. T., Uecker, M., Lustig, M., Pauly, J. M., Vasanawala, S. S. 2017; 7 (1): 5330

  Abstract

  Diagnostic testing often assesses the cardiovascular or respiratory systems in isolation, ignoring the major pathophysiologic interactions between the systems in many diseases. When both systems are assessed currently, multiple modalities are utilized in costly fashion with burdensome logistics and decreased accessibility. Thus, we have developed a new acquisition and reconstruction paradigm using the flexibility of MRI to enable a comprehensive exam from a single 5-15 min scan. We constructed a compressive-sensing approach to pseudo-randomly acquire highly subsampled, multi-dimensionally-encoded and time-stamped data from which we reconstruct volumetric cardiac and respiratory motion phases, contrast-agent dynamics, and blood flow velocity fields. The proposed method, named XD flow, is demonstrated for (a) evaluating congenital heart disease, where the impact of bulk motion is reduced in a non-sedated neonatal patient and (b) where the observation of the impact of respiration on flow is necessary for diagnostics; (c) cardiopulmonary imaging, where cardiovascular flow, function, and anatomy information is needed along with pulmonary perfusion quantification; and in (d) renal function imaging, where blood velocities and glomerular filtration rates are simultaneously measured, which highlights the generality of the technique. XD flow has the ability to improve quantification and to provide additional data for patient diagnosis for comprehensive evaluations.

  View details for DOI 10.1038/s41598-017-04676-8

  View details for PubMedID 28706270

  View details for PubMedCentralID PMC5509743

• Resolving phase ambiguity in dual-echo dixon imaging using a projected power method MAGNETIC RESONANCE IN MEDICINE Zhang, T., Chen, Y., Bao, S., Alley, M. T., Pauly, J. M., Hargreaves, B. A., Vasanawala, S. S. 2017; 77 (5): 2066-2076

  Abstract

  To develop a fast and robust method to resolve phase ambiguity in dual-echo Dixon imaging.A major challenge in dual-echo Dixon imaging is to estimate the phase error resulting from field inhomogeneity. In this work, a binary quadratic optimization program was formulated to resolve the phase ambiguity. A projected power method was developed to efficiently solve the optimization problem. Both the 1-peak fat model and 6-peak fat model were applied to three-dimensional (3D) datasets. Additionally, the proposed method was extended to dynamic magnetic resonance imaging (MRI) applications using the 6-peak fat model. With institutional review board (IRB) approval and patient consent/assent, the proposed method was evaluated and compared with region growing on 29 consecutive 3D high-resolution patient datasets.Fast and robust water/fat separation was achieved by the proposed method in different representative 3D datasets and dynamic 3D datasets. Superior water/fat separation was achieved using the 6-peak fat model compared with the 1-peak fat model. Compared to region growing, the proposed method reduced water/fat swaps from 76 to 7% of the patient cohort.The proposed method can achieve fast and robust phase error estimation in dual-echo Dixon imaging. Magn Reson Med, 2016. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.26287

  View details for Web of Science ID 000399666400034

  View details for PubMedCentralID PMC5123983

• Slice profile effects on nCPMG SS-FSE. Magnetic resonance in medicine Gibbons, E. K., Le Roux, P., Pauly, J. M., Kerr, A. B. 2017

  Abstract

  To determine the effects of the RF refocusing pulse profile on the magnitude of the transverse signal smoothness throughout the echo train in non-Carr-Purcell-Meiboom-Gill (nCPMG) single-shot fast spin echo (SS-FSE) imaging and to design an RF refocusing pulse that provides improved signal stability. THEORY AND METHODS: nCPMG SS-FSE quadratic phase modulation requires sufficiently high and uniform refocusing flip angle to achieve a stable signal. Typically, refocusing pulses used in SS-FSE sequences are designed for minimum duration to minimize echo spacing and as a consequence have poor selectivity. However, delay-insensitive variable rate excitation Shinnar-Le Roux (DV-SLR) refocusing pulses can achieve both improved selectivity as well as a short duration. This class of RF pulse is compared against a traditional low time-bandwidth refocusing pulse in a nCPMG SS-FSE in simulation, phantom, and in vivo.DV-SLR pulses achieve a more stable signal in simulation, phantom, and in vivo cases while maintaining an appropriately short duration as well as not dramatically increasing specific absorption rate (SAR) accumulation.The nCPMG SS-FSE method demonstrates improved robustness when a more selective refocusing pulse is used. Refocusing pulses that use a time-varying excitation gradient can achieve this selectivity while maintaining short echo spacing. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine.

  View details for DOI 10.1002/mrm.26694

  View details for PubMedID 28370409

• Improved cortical bone specificity in UTE MR Imaging MAGNETIC RESONANCE IN MEDICINE Johnson, E. M., Vyas, U., Ghanouni, P., Pauly, K. B., Pauly, J. M. 2017; 77 (2): 684-695

  Abstract

  Methods for direct visualization of compact bone using MRI have application in several "MR-informed" technologies, such as MR-guided focused ultrasound, MR-PET reconstruction and MR-guided radiation therapy. The specificity of bone imaging can be improved by manipulating image sensitivity to Bloch relaxation phenomena, facilitating distinction of bone from other tissues detected by MRI.From Bloch equation dynamics, excitation pulses suitable for creating specific sensitivity to short-T2 magnetization from cortical bone are identified. These pulses are used with UTE subtraction demonstrate feasibility of MR imaging of compact bone with positive contrast.MR images of bone structures are acquired with contrast similar to that observed in x-ray CT images. Through comparison of MR signal intensities with CT Hounsfield units of the skull, the similarity of contrast is quantified. The MR technique is also demonstrated in other regions of the body that are relevant for interventional procedures, such as the shoulder, pelvis and leg.Matching RF excitation pulses to relaxation rates improves the specificity to bone of short-T2 contrast. It is demonstrated with a UTE sequence to acquire images of cortical bone with positive contrast, and the contrast is verified by comparison with x-ray CT. Magn Reson Med, 2016. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.26160

  View details for Web of Science ID 000394544700025

  View details for PubMedCentralID PMC5040625

• A Millimeter-Wave Digital Link for Wireless MRI IEEE TRANSACTIONS ON MEDICAL IMAGING Aggarwal, K., Joshi, K. R., Rajavi, Y., Taghivand, M., Pauly, J. M., Poon, A. S., Scott, G. 2017; 36 (2): 574-583

  Abstract

  A millimeter (mm) wave radio is presented in this work to support wireless MRI data transmission. High path loss and availability of wide bandwidth make mm-waves an ideal candidate for short range, high data rata communication required for wireless MRI. The proposed system uses a custom designed integrated chip (IC) mm-wave radio with 60 GHz as radio frequency carrier. In this work, we assess performance in a 1.5 T MRI field, with the addition of optical links between the console room and magnet. The system uses ON-OFF keying (OOK) modulation for data transmission and supports data rates from 200 Mb/s to 2.5 Gb/s for distances up-to 65 cm. The presence of highly directional, linearly polarized, on-chip dipole antennas on the mm-wave radio along with the time division multiplexing (TDM) circuitry allows multiple wireless links to be created simultaneously with minimal inter-channel interference. This leads to a highly scalable solution for wireless MRI.

  View details for DOI 10.1109/TMI.2016.2622251

  View details for Web of Science ID 000396115800021

  View details for PubMedCentralID PMC5709036

• Body Diffusion Weighted Imaging Using Non-CPMG Fast Spin Echo IEEE TRANSACTIONS ON MEDICAL IMAGING Gibbons, E. K., Le Roux, P., Vasanawala, S. S., Pauly, J. M., Kerr, A. B. 2017; 36 (2): 549-559

  Abstract

  SS-FSE is a fast technique that does not suffer from off-resonance distortions to the degree that EPI does. Unlike EPI, SS-FSE is ill-suited to diffusion weighted imaging (DWI) due to the Carr-Purcell-Meiboom-Geill (CPMG) condition. Non- CPMG phase cycling does accommodate SS-FSE and DWI but places constraints on reconstruction, which are resolved here through parallel imaging. Additionally, improved echo stability can be achieved by using short duration and highly selective DIVERSE radiofrequency pulses. Here, signal-to-noise ratio (SNR) comparisons between EPI and nCPMG SS-FSE acquisitions and reconstruction techniques give similar values. Diffusion imaging with nCPMG SS-FSE gives similar SNR to an EPI acquisition, though apparent diffusion coefficient values are higher than seen with EPI. In vivo images have good image quality with little distortion. This method has the ability to capture distortionfree DWI images near areas of significant off-resonance as well as preserve adequate SNR. Parallel imaging and DIVERSE refocusing RF pulses allow shorter ETL compared to previous implementations and thus reduces phase encode direction blur and SAR accumulation.

  View details for DOI 10.1109/TMI.2016.2622238

  View details for Web of Science ID 000396115800019

• Formulation of image fusion as a constrained least squares optimization problem. Journal of medical imaging (Bellingham, Wash.) Dwork, N., Lasry, E. M., Pauly, J. M., Balbás, J. 2017; 4 (1): 014003-?

  Abstract

  Fusing a lower resolution color image with a higher resolution monochrome image is a common practice in medical imaging. By incorporating spatial context and/or improving the signal-to-noise ratio, it provides clinicians with a single frame of the most complete information for diagnosis. In this paper, image fusion is formulated as a convex optimization problem that avoids image decomposition and permits operations at the pixel level. This results in a highly efficient and embarrassingly parallelizable algorithm based on widely available robust and simple numerical methods that realizes the fused image as the global minimizer of the convex optimization problem.

  View details for DOI 10.1117/1.JMI.4.1.014003

  View details for PubMedID 28331885

• Frequency shifting reduces but does not eliminate acoustic interference between echolocating bats: A theoretical analysis The Journal of the Acoustical Society of America Perkins, M. L., Frank, H. K., Pauly, J. M., Hadly, E. A. 2017; 142: 2133

  Abstract

  Bats have been observed to shift the frequency of their echolocation calls in the presence of other echolocating bats, ostensibly as a way to reduce acoustic interference. Few studies, however, have examined the theoretical efficacy of such jamming avoidance responses. The present study uses the wideband ambiguity function to analyze the effects of acoustic interference from conspecifics and congeneric heterospecifics on the target acquisition ability of Myotis californicus and Myotis yumanensis, specifically whether unilateral or bilateral frequency shifts reduce the effects of such interference. Model results suggest that in conspecific interactions, M. yumanensis recovers its target acquisition ability more completely and with less absolute frequency shift than does M. californicus, but that alternative methods of jamming avoidance may be easier to implement. The optimal strategy for reducing heterospecific interference is for M. californicus to downshift its call and M. yumanensis to upshift its call, which exaggerates a preexisting difference in mean frequency between the calls of the two species. Further empirical research would elucidate whether these species do in practice actively employ frequency shifting or other means for jamming avoidance, as well as illuminate the role of acoustic interference in niche partitioning.

  View details for DOI 10.1121/1.5006928

• Recurrent Generative Adversarial Neural Networks for Compressive Imaging Mardani, M., Gong, E., Cheng, J. Y., Pauly, J., Xing, L., IEEE IEEE. 2017

  View details for Web of Science ID 000428438100153

• Autocalibrating motion-corrected wave-encoding for highly accelerated free-breathing abdominal MRI. Magnetic resonance in medicine Chen, F., Zhang, T., Cheng, J. Y., Shi, X., Pauly, J. M., Vasanawala, S. S. 2016

  Abstract

  To develop a motion-robust wave-encoding technique for highly accelerated free-breathing abdominal MRI.A comprehensive 3D wave-encoding-based method was developed to enable fast free-breathing abdominal imaging: (a) auto-calibration for wave-encoding was designed to avoid extra scan for coil sensitivity measurement; (b) intrinsic butterfly navigators were used to track respiratory motion; (c) variable-density sampling was included to enable compressed sensing; (d) golden-angle radial-Cartesian hybrid view-ordering was incorporated to improve motion robustness; and (e) localized rigid motion correction was combined with parallel imaging compressed sensing reconstruction to reconstruct the highly accelerated wave-encoded datasets. The proposed method was tested on six subjects and image quality was compared with standard accelerated Cartesian acquisition both with and without respiratory triggering. Inverse gradient entropy and normalized gradient squared metrics were calculated, testing whether image quality was improved using paired t-tests.For respiratory-triggered scans, wave-encoding significantly reduced residual aliasing and blurring compared with standard Cartesian acquisition (metrics suggesting P < 0.05). For non-respiratory-triggered scans, the proposed method yielded significantly better motion correction compared with standard motion-corrected Cartesian acquisition (metrics suggesting P < 0.01).The proposed methods can reduce motion artifacts and improve overall image quality of highly accelerated free-breathing abdominal MRI. Magn Reson Med, 2016. © 2016 International Society for Magnetic Resonance in Medicine.

  View details for DOI 10.1002/mrm.26567

  View details for PubMedID 27943402

• Depletion-Mode GaN HEMT Q-Spoil Switches for MRI Coils IEEE TRANSACTIONS ON MEDICAL IMAGING Lu, J. Y., Grafendorfer, T., Zhang, T., Vasanawala, S., Robb, F., Pauly, J. M., Scott, G. C. 2016; 35 (12): 2558-2567

  Abstract

  Q-spoiling is the process of decoupling an MRI receive coil to protect the equipment and patient. Conventionally, Q-spoiling is performed using a PIN diode switch that draws significant current. In this work, a Q-spoiling technique using a depletion-mode Gallium Nitride HEMT device was developed for coil detuning at both 1.5 T and 3 T MRI. The circuits with conventional PIN diode Q-spoiling and the GaN HEMT device were implemented on surface coils. SNR was measured and compared for all surfaces coils. At both 1.5 T and 3 T, comparable SNR was achieved for all coils with the proposed technique and conventional Q-spoiling. The GaN HEMT device has significantly reduced the required power for Q-spoiling. The GaN HEMT device also provides useful safety features by detuning the coil when unpowered.

  View details for DOI 10.1109/TMI.2016.2586053

  View details for Web of Science ID 000391547700005

  View details for PubMedID 27362895

• Body diffusion weighted imaging using non-CPMG fast spin echo. IEEE transactions on medical imaging Gibbons, E., Le Roux, P., Vasanawala, S., Pauly, J., Kerr, A. 2016: -?

  Abstract

  SS-FSE is a fast technique that does not suffer from off-resonance distortions to the degree that EPI does. Unlike EPI, SS-FSE is ill-suited to diffusion weighted imaging (DWI) due to the Carr-Purcell-Meiboom-Geill (CPMG) condition. Non- CPMG phase cycling does accommodate SS-FSE and DWI but places constraints on reconstruction, which are resolved here through parallel imaging. Additionally, improved echo stability can be achieved by using short duration and highly selective DIVERSE radiofrequency pulses. Here, signal-to-noise ratio (SNR) comparisons between EPI and nCPMG SS-FSE acquisitions and reconstruction techniques give similar values. Diffusion imaging with nCPMG SS-FSE gives similar SNR to an EPI acquisition, though apparent diffusion coefficient values are higher than seen with EPI. In vivo images have good image quality with little distortion. This method has the ability to capture distortionfree DWI images near areas of significant off-resonance as well as preserve adequate SNR. Parallel imaging and DIVERSE refocusing RF pulses allow shorter ETL compared to previous implementations and thus reduces phase encode direction blur and SAR accumulation.

  View details for PubMedID 27810802

• Spectrally selective three-dimensional dynamic balanced steady-state free precession for hyperpolarized C-13 metabolic imaging with spectrally selective radiofrequency pulses. Magnetic resonance in medicine Shang, H., Sukumar, S., Von Morze, C., Bok, R. A., Marco-Rius, I., Kerr, A., Reed, G. D., Milshteyn, E., Ohliger, M. A., Kurhanewicz, J., Larson, P. E., Pauly, J. M., Vigneron, D. B. 2016

  Abstract

  Balanced steady-state free precession (bSSFP) sequences can provide superior signal-to-noise ratio efficiency for hyperpolarized (HP) carbon-13 ((13) C) magnetic resonance imaging by efficiently utilizing the nonrecoverable magnetization, but managing their spectral response is challenging in the context of metabolic imaging. A new spectrally selective bSSFP sequence was developed for fast imaging of multiple HP (13) C metabolites with high spatiotemporal resolution.This novel approach for bSSFP spectral selectivity incorporates optimized short-duration spectrally selective radiofrequency pulses within a bSSFP pulse train and a carefully chosen repetition time to avoid banding artifacts.The sequence enabled subsecond 3D dynamic spectrally selective imaging of (13) C metabolites of copolarized [1-(13) C]pyruvate and [(13) C]urea at 2-mm isotropic resolution, with excellent spectral selectivity (∼100:1). The sequence was successfully tested in phantom studies and in vivo studies with normal mice.This sequence is expected to benefit applications requiring dynamic volumetric imaging of metabolically active (13) C compounds at high spatiotemporal resolution, including preclinical studies at high field and, potentially, clinical studies.Magn Reson Med, 2016. © 2016 International Society for Magnetic Resonance in Medicine.

  View details for DOI 10.1002/mrm.26480

  View details for PubMedID 27770458

• A semiflexible 64-channel receive-only phased array for pediatric body MRI at 3T. Magnetic resonance in medicine Zhang, T., Grafendorfer, T., Cheng, J. Y., Ning, P., Rainey, B., Giancola, M., Ortman, S., Robb, F. J., Calderon, P. D., Hargreaves, B. A., Lustig, M., Scott, G. C., Pauly, J. M., Vasanawala, S. S. 2016; 76 (3): 1015-1021

  Abstract

  To design, construct, and validate a semiflexible 64-channel receive-only phased array for pediatric body MRI at 3T.A 64-channel receive-only phased array was developed and constructed. The designed flexible coil can easily conform to different patient sizes with nonoverlapping coil elements in the transverse plane. It can cover a field of view of up to 44 × 28 cm(2) and removes the need for coil repositioning for body MRI patients with multiple clinical concerns. The 64-channel coil was compared with a 32-channel standard coil for signal-to-noise ratio and parallel imaging performances on different phantoms. With IRB approval and informed consent/assent, the designed coil was validated on 21 consecutive pediatric patients.The pediatric coil provided higher signal-to-noise ratio than the standard coil on different phantoms, with the averaged signal-to-noise ratio gain at least 23% over a depth of 7 cm along the cross-section of phantoms. It also achieved better parallel imaging performance under moderate acceleration factors. Good image quality (average score 4.6 out of 5) was achieved using the developed pediatric coil in the clinical studies.A 64-channel semiflexible receive-only phased array has been developed and validated to facilitate high quality pediatric body MRI at 3T. Magn Reson Med 76:1015-1021, 2016. © 2015 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.25999

  View details for PubMedID 26418283

  View details for PubMedCentralID PMC4811745

• Hybrid-Space SENSE Reconstruction for Simultaneous Multi-Slice MRI IEEE TRANSACTIONS ON MEDICAL IMAGING Zhu, K., Dougherty, R. F., Wu, H., Middione, M. J., Takahashi, A. M., Zhang, T., Pauly, J. M., Kerr, A. B. 2016; 35 (8): 1824-1836

  Abstract

  Simultaneous Multi-Slice (SMS) magnetic resonance imaging (MRI) is a rapidly evolving technique for increasing imaging speed. Controlled aliasing techniques utilize periodic undersampling patterns to help mitigate the loss in signal-to-noise ratio (SNR) in SMS MRI. To evaluate the performance of different undersampling patterns, a quantitative description of the image SNR loss is needed. Additionally, eddy current effects in echo planar imaging (EPI) lead to slice-specific Nyquist ghosting artifacts. These artifacts cannot be accurately corrected for each individual slice before or after slice-unaliasing. In this work, we propose a hybrid-space sensitivity encoding (SENSE) reconstruction framework for SMS MRI by adopting a three-dimensional representation of the SMS acquisition. Analytical SNR loss maps are derived for SMS acquisitions with arbitrary phase encoding undersampling patterns. Moreover, we propose a matrix-decoding correction method that corrects the slice-specific Nyquist ghosting artifacts in SMS EPI acquisitions. Brain images demonstrate that the proposed hybrid-space SENSE reconstruction generates images with comparable quality to commonly used split-slice-generalized autocalibrating partially parallel acquisition reconstruction. The analytical SNR loss maps agree with those calculated by a Monte Carlo based method, but require less computation time for high quality maps. The analytical maps enable a fair comparison between the performances of coherent and incoherent SMS undersampling patterns. Phantom and brain SMS EPI images show that the matrix-decoding method performs better than the single-slice and slice-averaged Nyquist ghosting correction methods under the hybrid-space SENSE reconstruction framework.

  View details for DOI 10.1109/TMI.2016.2531635

  View details for Web of Science ID 000381436000004

  View details for PubMedID 26915118

  View details for PubMedCentralID PMC4988924

• Robust self-navigated body MRI using dense coil arrays. Magnetic resonance in medicine Zhang, T., Cheng, J. Y., Chen, Y., Nishimura, D. G., Pauly, J. M., Vasanawala, S. S. 2016; 76 (1): 197-205

  Abstract

  To develop a robust motion estimation method for free-breathing body MRI using dense coil arrays.Self-navigating pulse sequences can measure subject motion without using external motion monitoring devices. With dense coil arrays, individual coil elements can provide localized motion estimates. An averaged motion estimate over all coils is often used for motion compensation. However, this motion estimate may not accurately represent the dominant motion within the imaging volume. In this work, a coil clustering method is proposed to automatically determine the dominant motion for dense coil arrays. The feasibility of the proposed method is investigated in free-breathing abdominal MRI and cardiac MRI, and compared with manual motion estimate selection for respiratory motion estimation and electrocardiography for cardiac motion estimation.Automated motion estimation achieved similar respiratory motion estimation compared to manual selection (averaged correlation coefficient 0.989 and 0.988 for abdominal MRI and cardiac MRI, respectively), and accurate cardiac triggering compared to electrocardiography (averaged temporal variability 17.5 ms).The proposed method can provide accurate automated motion estimation for body MRI using dense coil arrays. It can enable self-navigated free-breathing abdominal and cardiac MRI without the need for external motion monitoring devices. Magn Reson Med 76:197-205, 2016. © 2015 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.25858

  View details for PubMedID 26220204

  View details for PubMedCentralID PMC4732937

• Comprehensive motion-compensated highly accelerated 4D flow MRI with ferumoxytol enhancement for pediatric congenital heart disease. Journal of magnetic resonance imaging Cheng, J. Y., Hanneman, K., Zhang, T., Alley, M. T., Lai, P., Tamir, J. I., Uecker, M., Pauly, J. M., Lustig, M., Vasanawala, S. S. 2016; 43 (6): 1355-1368

  Abstract

  To develop and evaluate motion-compensation and compressed-sensing techniques in 4D flow MRI for anatomical assessment in a comprehensive ferumoxytol-enhanced congenital heart disease (CHD) exam.A Cartesian 4D flow sequence was developed to enable intrinsic navigation and two variable-density sampling schemes: VDPoisson and VDRad. Four compressed-sensing methods were developed: A) VDPoisson scan reconstructed using spatial wavelets; B) added temporal total variation to A; C) VDRad scan using the same reconstruction as in B; and D) added motion compensation to C. With Institutional Review Board (IRB) approval and Health Insurance Portability and Accountability Act (HIPAA) compliance, 23 consecutive patients (eight females, mean 6.3 years) referred for ferumoxytol-enhanced CHD 3T MRI were recruited. Images were acquired and reconstructed using methods A-D. Two cardiovascular radiologists independently scored the images on a 5-point scale. These readers performed a paired wall motion and functional assessment between method D and 2D balanced steady-state free precession (bSSFP) CINE for 16 cases.Method D had higher diagnostic image quality for most anatomical features (mean 3.8-4.8) compared to A (2.0-3.6), B (2.2-3.7), and C (2.9-3.9) with P < 0.05 with good interobserver agreement (κ ≥ 0.49). Method D had similar or better assessment of myocardial borders and cardiac motion compared to 2D bSSFP (P < 0.05, κ ≥ 0.77). All methods had good internal agreement in comparing aortic with pulmonic flow (BA mean < 0.02%, r > 0.85) and compared to method A (BA mean < 0.13%, r > 0.84) with P < 0.01.Flow, functional, and anatomical assessment in CHD with ferumoxytol-enhanced 4D flow is feasible and can be significantly improved using motion compensation and compressed sensing. J. Magn. Reson. Imaging 2016;43:1355-1368.

  View details for DOI 10.1002/jmri.25106

  View details for PubMedID 26646061

  View details for PubMedCentralID PMC4865413

• Resolving phase ambiguity in dual-echo dixon imaging using a projected power method. Magnetic resonance in medicine Zhang, T., Chen, Y., Bao, S., Alley, M. T., Pauly, J. M., Hargreaves, B. A., Vasanawala, S. S. 2016

  Abstract

  To develop a fast and robust method to resolve phase ambiguity in dual-echo Dixon imaging.A major challenge in dual-echo Dixon imaging is to estimate the phase error resulting from field inhomogeneity. In this work, a binary quadratic optimization program was formulated to resolve the phase ambiguity. A projected power method was developed to efficiently solve the optimization problem. Both the 1-peak fat model and 6-peak fat model were applied to three-dimensional (3D) datasets. Additionally, the proposed method was extended to dynamic magnetic resonance imaging (MRI) applications using the 6-peak fat model. With institutional review board (IRB) approval and patient consent/assent, the proposed method was evaluated and compared with region growing on 29 consecutive 3D high-resolution patient datasets.Fast and robust water/fat separation was achieved by the proposed method in different representative 3D datasets and dynamic 3D datasets. Superior water/fat separation was achieved using the 6-peak fat model compared with the 1-peak fat model. Compared to region growing, the proposed method reduced water/fat swaps from 76 to 7% of the patient cohort.The proposed method can achieve fast and robust phase error estimation in dual-echo Dixon imaging. Magn Reson Med, 2016. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.26287

  View details for PubMedID 27221766

  View details for PubMedCentralID PMC5123983

• Fat-suppressed alternating-SSFP for whole-brain fMRI using breath-hold and visual stimulus paradigms. Magnetic resonance in medicine Jou, T., Patterson, S., Pauly, J. M., Bowen, C. V. 2016; 75 (5): 1978-1988

  Abstract

  To achieve artifact-suppressed whole-brain pass-band-balanced steady-state free precession functional MRI from a single functional magnetic resonance imaging (fMRI) scan.A complete and practical data acquisition sequence for alt-SSFP fMRI was developed. First, multishot flyback-echo-planar imaging (EPI) and echo-time shifting were used to achieve data acquisition that was robust against eddy currents, gradient delays, and ghosting artifacts. Second, a steady-state catalyzation scheme was implemented to reduce oscillations in the transient signal when catalyzing in and out of alternate steady states. Next, a short spatial-spectral radiofrequency (RF) pulse was designed to achieve excellent fat-suppression while maintaining a repetition time <15 ms to sensitize functional activation toward smaller vessels and capillaries. Lastly, parallel imaging was used to achieve whole-brain coverage and sufficiently high temporal resolution.Breath-hold experiments showed excellent fat-suppression and alt-SSFP's capability to recover functional sensitivity from signal dropout regions of conventional gradient-echo and banding artifacts from conventional pass-band-balanced steady-state free precession. Applying fat-suppression resulted in improved activation maps and increased temporal SNR. Visual stimulus functional studies verify the proposed method's excellent functional sensitivity to neuronal activation.Artifact-suppressed images are demonstrated, showing a practical pass-band-balanced steady-state free precession fMRI method that permits whole-brain imaging with excellent blood oxygen level-dependent sensitivity and fat suppression. Magn Reson Med 75:1978-1988, 2016. © 2015 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.25797

  View details for PubMedID 26037220

  View details for PubMedCentralID PMC4746113

• Improved cortical bone specificity in UTE MR Imaging. Magnetic resonance in medicine Johnson, E. M., Vyas, U., Ghanouni, P., Pauly, K. B., Pauly, J. M. 2016

  Abstract

  Methods for direct visualization of compact bone using MRI have application in several "MR-informed" technologies, such as MR-guided focused ultrasound, MR-PET reconstruction and MR-guided radiation therapy. The specificity of bone imaging can be improved by manipulating image sensitivity to Bloch relaxation phenomena, facilitating distinction of bone from other tissues detected by MRI.From Bloch equation dynamics, excitation pulses suitable for creating specific sensitivity to short-T2 magnetization from cortical bone are identified. These pulses are used with UTE subtraction demonstrate feasibility of MR imaging of compact bone with positive contrast.MR images of bone structures are acquired with contrast similar to that observed in x-ray CT images. Through comparison of MR signal intensities with CT Hounsfield units of the skull, the similarity of contrast is quantified. The MR technique is also demonstrated in other regions of the body that are relevant for interventional procedures, such as the shoulder, pelvis and leg.Matching RF excitation pulses to relaxation rates improves the specificity to bone of short-T2 contrast. It is demonstrated with a UTE sequence to acquire images of cortical bone with positive contrast, and the contrast is verified by comparison with x-ray CT. Magn Reson Med, 2016. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.26160

  View details for PubMedID 26972442

  View details for PubMedCentralID PMC5040625

• Development and testing of hyperpolarized (13)C MR calibrationless parallel imaging. Journal of magnetic resonance Feng, Y., Gordon, J. W., Shin, P. J., Von Morze, C., Lustig, M., Larson, P. E., Ohliger, M. A., Carvajal, L., Tropp, J., Pauly, J. M., Vigneron, D. B. 2016; 262: 1-7

  Abstract

  A calibrationless parallel imaging technique developed previously for (1)H MRI was modified and tested for hyperpolarized (13)C MRI for applications requiring large FOV and high spatial resolution. The technique was demonstrated with both retrospective and prospective under-sampled data acquired in phantom and in vivo rat studies. A 2-fold acceleration was achieved using a 2D symmetric EPI readout equipped with random blips on the phase encode dimension. Reconstructed images showed excellent qualitative agreement with fully sampled data. Further acceleration can be achieved using acquisition schemes that incorporate multi-dimensional under-sampling.

  View details for DOI 10.1016/j.jmr.2015.10.018

  View details for PubMedID 26679288

  View details for PubMedCentralID PMC4864033

• Multiband RF pulses with improved performance via convex optimization JOURNAL OF MAGNETIC RESONANCE Shang, H., Larson, P. E., Kerr, A., Reed, G., Sukumar, S., Elkhaled, A., Gordon, J. W., Ohliger, M. A., Pauly, J. M., Lustig, M., Vigneron, D. B. 2016; 262: 81-90

  Abstract

  Selective RF pulses are commonly designed with the desired profile as a low pass filter frequency response. However, for many MRI and NMR applications, the spectrum is sparse with signals existing at a few discrete resonant frequencies. By specifying a multiband profile and releasing the constraint on "don't-care" regions, the RF pulse performance can be improved to enable a shorter duration, sharper transition, or lower peak B1 amplitude. In this project, a framework for designing multiband RF pulses with improved performance was developed based on the Shinnar-Le Roux (SLR) algorithm and convex optimization. It can create several types of RF pulses with multiband magnitude profiles, arbitrary phase profiles and generalized flip angles. The advantage of this framework with a convex optimization approach is the flexible trade-off of different pulse characteristics. Designs for specialized selective RF pulses for balanced SSFP hyperpolarized (HP) (13)C MRI, a dualband saturation RF pulse for (1)H MR spectroscopy, and a pre-saturation pulse for HP (13)C study were developed and tested.

  View details for DOI 10.1016/j.jmr.2015.11.010

  View details for Web of Science ID 000369877700013

  View details for PubMedID 26754063

  View details for PubMedCentralID PMC4716678

• Automated, Depth-Resolved Estimation of the Attenuation Coefficient From Optical Coherence Tomography Data IEEE TRANSACTIONS ON MEDICAL IMAGING Smith, G. T., Dwork, N., O'Connor, D., Sikora, U., Lurie, K. L., Pauly, J. M., Ellerbee, A. K. 2015; 34 (12): 2592-2602

  View details for DOI 10.1109/TMI.2015.2450197

  View details for Web of Science ID 000366104500015

• Controlling radiofrequency-induced currents in guidewires using parallel transmit. Magnetic resonance in medicine Etezadi-Amoli, M., Stang, P., Kerr, A., Pauly, J., Scott, G. 2015; 74 (6): 1790-802

  Abstract

  Elongated conductors, such as pacemaker leads, neurostimulator leads, and conductive guidewires used for interventional procedures can couple to the MRI radiofrequency (RF) transmit field, potentially causing dangerous tissue heating. The purpose of this study was to demonstrate the feasibility of using parallel transmit to control induced RF currents in elongated conductors, thereby reducing the RF heating hazard.Phantom experiments were performed on a four-channel parallel transmit system at 1.5T. Parallel transmit "null mode" excitations that induce minimal wire current were designed using coupling measurements derived from axial B1 (+) maps. The resulting current reduction performance was evaluated with B1 (+) maps, current sensor measurements, and fluoroptic temperature probe measurements.Null mode excitations reduced the maximum coupling mode current by factors ranging from 2 to 80. For the straight wire experiment, a current null imposed at a single wire location was sufficient to reduce tip heating below detectable levels. For longer insertion lengths and a curved geometry, imposing current nulls at two wire locations resulted in more distributed current reduction along the wire length.Parallel transmit can be used to create excitations that induce minimal RF current in elongated conductors, thereby decreasing the RF heating risk, while still allowing visualization of the surrounding volume.

  View details for DOI 10.1002/mrm.25543

  View details for PubMedID 25521751

  View details for PubMedCentralID PMC4470871

• Controlling Radiofrequency-Induced Currents in Guidewires Using Parallel Transmit MAGNETIC RESONANCE IN MEDICINE Etezadi-Amoli, M., Stang, P., Kerr, A., Pauly, J., Scott, G. 2015; 74 (6): 1790-1802

  Abstract

  Elongated conductors, such as pacemaker leads, neurostimulator leads, and conductive guidewires used for interventional procedures can couple to the MRI radiofrequency (RF) transmit field, potentially causing dangerous tissue heating. The purpose of this study was to demonstrate the feasibility of using parallel transmit to control induced RF currents in elongated conductors, thereby reducing the RF heating hazard.Phantom experiments were performed on a four-channel parallel transmit system at 1.5T. Parallel transmit "null mode" excitations that induce minimal wire current were designed using coupling measurements derived from axial B1 (+) maps. The resulting current reduction performance was evaluated with B1 (+) maps, current sensor measurements, and fluoroptic temperature probe measurements.Null mode excitations reduced the maximum coupling mode current by factors ranging from 2 to 80. For the straight wire experiment, a current null imposed at a single wire location was sufficient to reduce tip heating below detectable levels. For longer insertion lengths and a curved geometry, imposing current nulls at two wire locations resulted in more distributed current reduction along the wire length.Parallel transmit can be used to create excitations that induce minimal RF current in elongated conductors, thereby decreasing the RF heating risk, while still allowing visualization of the surrounding volume.

  View details for DOI 10.1002/mrm.25543

  View details for Web of Science ID 000367737300031

  View details for PubMedCentralID PMC4470871

• Clinical performance of a free-breathing spatiotemporally accelerated 3-D time-resolved contrast-enhanced pediatric abdominal MR angiography. Pediatric radiology Zhang, T., Yousaf, U., Hsiao, A., Cheng, J. Y., Alley, M. T., Lustig, M., Pauly, J. M., Vasanawala, S. S. 2015; 45 (11): 1635-1643

  Abstract

  Pediatric contrast-enhanced MR angiography is often limited by respiration, other patient motion and compromised spatiotemporal resolution.To determine the reliability of a free-breathing spatiotemporally accelerated 3-D time-resolved contrast-enhanced MR angiography method for depicting abdominal arterial anatomy in young children.With IRB approval and informed consent, we retrospectively identified 27 consecutive children (16 males and 11 females; mean age: 3.8 years, range: 14 days to 8.4 years) referred for contrast-enhanced MR angiography at our institution, who had undergone free-breathing spatiotemporally accelerated time-resolved contrast-enhanced MR angiography studies. A radio-frequency-spoiled gradient echo sequence with Cartesian variable density k-space sampling and radial view ordering, intrinsic motion navigation and intermittent fat suppression was developed. Images were reconstructed with soft-gated parallel imaging locally low-rank method to achieve both motion correction and high spatiotemporal resolution. Quality of delineation of 13 abdominal arteries in the reconstructed images was assessed independently by two radiologists on a five-point scale. Ninety-five percent confidence intervals of the proportion of diagnostically adequate cases were calculated. Interobserver agreements were also analyzed.Eleven out of 13 arteries achieved acceptable image quality (mean score range: 3.9-5.0) for both readers. Fair to substantial interobserver agreement was reached on nine arteries.Free-breathing spatiotemporally accelerated 3-D time-resolved contrast-enhanced MR angiography frequently yields diagnostic image quality for most abdominal arteries in young children.

  View details for DOI 10.1007/s00247-015-3384-y

  View details for PubMedID 26040509

  View details for PubMedCentralID PMC4580561

• Chemical Shift Separation with Controlled Aliasing for Hyperpolarized C-13 Metabolic Imaging MAGNETIC RESONANCE IN MEDICINE Shin, P. J., Larson, P. E., Uecker, M., Reed, G. D., Kerr, A. B., Tropp, J., Ohliger, M. A., Nelson, S. J., Pauly, J. M., Lustig, M., Vigneron, D. B. 2015; 74 (4): 978-989

  Abstract

  A chemical shift separation technique for hyperpolarized (13) C 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 (13) C species simultaneously with subsequent separation into individual images.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.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.This method demonstrated the ability to provide accelerated metabolite imaging in hyperpolarized (13) C MR using multichannel coils, tailored readout, and specialized RF pulses. Magn Reson Med 74:978-989, 2015. © 2014 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.25473

  View details for Web of Science ID 000364215200009

  View details for PubMedID 25298086

  View details for PubMedCentralID PMC4390401

• Free-breathing pediatric MRI with nonrigid motion correction and acceleration JOURNAL OF MAGNETIC RESONANCE IMAGING Cheng, J. Y., Zhang, T., Ruangwattanapaisarn, N., Alley, M. T., Uecker, M., Pauly, J. M., Lustig, M., Vasanawala, S. S. 2015; 42 (2): 407-420

  Abstract

  To develop and assess motion correction techniques for high-resolution pediatric abdominal volumetric magnetic resonance images acquired free-breathing with high scan efficiency.First, variable-density sampling and radial-like phase-encode ordering were incorporated into the 3D Cartesian acquisition. Second, intrinsic multichannel butterfly navigators were used to measure respiratory motion. Lastly, these estimates are applied for both motion-weighted data-consistency in a compressed sensing and parallel imaging reconstruction, and for nonrigid motion correction using a localized autofocusing framework. With Institutional Review Board approval and informed consent/assent, studies were performed on 22 consecutive pediatric patients. Two radiologists independently scored the images for overall image quality, degree of motion artifacts, and sharpness of hepatic vessels and the diaphragm. The results were assessed using paired Wilcoxon test and weighted kappa coefficient for interobserver agreements.The complete procedure yielded significantly better overall image quality (mean score of 4.7 out of 5) when compared to using no correction (mean score of 3.4, P < 0.05) and to using motion-weighted accelerated imaging (mean score of 3.9, P < 0.05). With an average scan time of 28 seconds, the proposed method resulted in comparable image quality to conventional prospective respiratory-triggered acquisitions with an average scan time of 91 seconds (mean score of 4.5).With the proposed methods, diagnosable high-resolution abdominal volumetric scans can be obtained from free-breathing data acquisitions. J. Magn. Reson. Imaging 2015;42:407-420.

  View details for DOI 10.1002/jmri.24785

  View details for Web of Science ID 000358258600019

  View details for PubMedCentralID PMC4404177

• Free-breathing pediatric MRI with nonrigid motion correction and acceleration. Journal of magnetic resonance imaging : JMRI Cheng, J. Y., Zhang, T., Ruangwattanapaisarn, N., Alley, M. T., Uecker, M., Pauly, J. M., Lustig, M., Vasanawala, S. S. 2015; 42 (2): 407-20

  Abstract

  To develop and assess motion correction techniques for high-resolution pediatric abdominal volumetric magnetic resonance images acquired free-breathing with high scan efficiency.First, variable-density sampling and radial-like phase-encode ordering were incorporated into the 3D Cartesian acquisition. Second, intrinsic multichannel butterfly navigators were used to measure respiratory motion. Lastly, these estimates are applied for both motion-weighted data-consistency in a compressed sensing and parallel imaging reconstruction, and for nonrigid motion correction using a localized autofocusing framework. With Institutional Review Board approval and informed consent/assent, studies were performed on 22 consecutive pediatric patients. Two radiologists independently scored the images for overall image quality, degree of motion artifacts, and sharpness of hepatic vessels and the diaphragm. The results were assessed using paired Wilcoxon test and weighted kappa coefficient for interobserver agreements.The complete procedure yielded significantly better overall image quality (mean score of 4.7 out of 5) when compared to using no correction (mean score of 3.4, P < 0.05) and to using motion-weighted accelerated imaging (mean score of 3.9, P < 0.05). With an average scan time of 28 seconds, the proposed method resulted in comparable image quality to conventional prospective respiratory-triggered acquisitions with an average scan time of 91 seconds (mean score of 4.5).With the proposed methods, diagnosable high-resolution abdominal volumetric scans can be obtained from free-breathing data acquisitions. J. Magn. Reson. Imaging 2015;42:407-420.

  View details for DOI 10.1002/jmri.24785

  View details for PubMedID 25329325

  View details for PubMedCentralID PMC4404177

• T1 rho Dispersion in Articular Cartilage: Relationship to Material Properties and Macromolecular Content CARTILAGE Keenan, K. E., Besier, T. F., Pauly, J. M., Smith, R. L., Delp, S. L., Beaupre, G. S., Gold, G. E. 2015; 6 (2): 113-122

  Abstract

  This study assessed T1ρ relaxation dispersion, measured by magnetic resonance imaging (MRI), as a tool to noninvasively evaluate cartilage material and biochemical properties. The specific objective was to answer two questions: (1) does cartilage initial elastic modulus (E 0) correlate with T1ρ dispersion effects and (2) does collagen or proteoglycan content correlate with T1ρ dispersion effects?Cadaveric patellae with and without visible cartilage damage on conventional MR were included. T2 and T1ρ relaxation times at 500 and 1000 Hz spin-lock field amplitudes were measured. We estimated T1ρ dispersion effects by measuring T1ρ relaxation time at 500 and 1000 Hz and T2 relaxation time and using a new tool, the ratio T1ρ/T2. Cartilage initial elastic modulus, E 0, was measured from initial response of mechanical indentation creep tests. Collagen and proteoglycan contents were measured at the indentation test sites; proteoglycan content was measured by their covalently linked sulfated glycosaminoglycans (sGAG). Pearson correlation coefficients were determined, taking into account the clustering of multiple samples within a single patella specimen.Cartilage initial elastic modulus, E 0, increased with decreasing values of T1ρ/T2 measurements at both 500 Hz (P = 0.034) and 1000 Hz (P = 0.022). 1/T1ρ relaxation time (500 Hz) increased with increasing sGAG content (P = 0.041).T1ρ/T2 ratio, a new tool, and cartilage initial elastic modulus are both measures of water-protein interactions, are dependent on the cartilage structure, and were correlated in this study.

  View details for DOI 10.1177/1947603515569529

  View details for Web of Science ID 000356631400006

  View details for PubMedID 26069714

  View details for PubMedCentralID PMC4462251

• Offline Impedance Measurements for Detection and Mitigation of Dangerous Implant Interactions: An RF Safety Prescreen MAGNETIC RESONANCE IN MEDICINE Ellenor, C. W., Stang, P. P., Etezadi-Amoli, M., Pauly, J. M., Scott, G. C. 2015; 73 (3): 1328-1339

  Abstract

  The concept of a "radiofrequency safety prescreen" is investigated, wherein dangerous interactions between radiofrequency fields used in MRI, and conductive implants in patients are detected through impedance changes in the radiofrequency coil.The behavior of coupled oscillators is reviewed, and the resulting, observable impedance changes are discussed.A birdcage coil is loaded with a static head phantom and a wire phantom with a wire close to its resonant length, the shape, position, and orientation of which can be changed. Interactions are probed with a current sensor and network analyzer.Impedance spectra show dramatic, unmistakable splitting in cases of strong coupling, and strong correlation is observed between induced current and scattering parameters.The feasibility of a new, low-power prescreening technique has been demonstrated in a simple phantom experiment, which can unambiguously detect resonant interactions between an implanted wire and an imaging coil. A new technique has also been presented which can detect parallel transmit null modes for the wire.

  View details for DOI 10.1002/mrm.25202

  View details for Web of Science ID 000350279900047

  View details for PubMedID 24623586

  View details for PubMedCentralID PMC4162873

• Interventional Device Visualization with Toroidal Transceiver and Optically Coupled Current Sensor for Radiofrequency Safety Monitoring MAGNETIC RESONANCE IN MEDICINE Etezadi-Amoli, M., Stang, P., Kerr, A., Pauly, J., Scott, G. 2015; 73 (3): 1315-1327

  Abstract

  The development of catheters and guidewires that are safe from radiofrequency (RF) -induced heating and clearly visible against background tissue is a major challenge in interventional MRI. An interventional imaging approach using a toroidal transmit-receive (transceive) coil is presented. This toroidal transceiver allows controlled, low levels of RF current to flow in the catheter/guidewire for visualization, and can be used with conductive interventional devices that have a localized low-impedance tip contact.Toroidal transceivers were built, and phantom experiments were performed to quantify transmit power levels required for device visibility and to detect heating hazards. Imaging experiments in a pig cadaver tested the extendibility to higher field strength and nonphantom settings. A photonically powered optically coupled toroidal current sensor for monitoring induced RF currents was built, calibrated, and tested using an independent image-based current estimation method.Results indicate that high signal-to-noise ratio visualization is achievable using milliwatts of transmit power-power levels orders of magnitude lower than levels that induce measurable heating in phantom tests. Agreement between image-based current estimates and RF current sensor measurements validates sensor accuracy.The toroidal transceiver, integrated with power and current sensing, could offer a promising platform for safe and effective interventional device visualization.

  View details for DOI 10.1002/mrm.25187

  View details for Web of Science ID 000350279900046

  View details for PubMedID 24691876

  View details for PubMedCentralID PMC4182300

• Fast pediatric 3D free-breathing abdominal dynamic contrast enhanced MRI with high spatiotemporal resolution. Journal of magnetic resonance imaging Zhang, T., Cheng, J. Y., Potnick, A. G., Barth, R. A., Alley, M. T., Uecker, M., Lustig, M., Pauly, J. M., Vasanawala, S. S. 2015; 41 (2): 460-473

  Abstract

  To develop a method for fast pediatric 3D free-breathing abdominal dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) and investigate its clinical feasibility.A combined locally low rank parallel imaging method with soft gating is proposed for free-breathing DCE MRI acquisition. With Institutional Review Board (IRB) approval and informed consent/assent, 23 consecutive pediatric patients were recruited for this study. Free-breathing DCE MRI with ∼1 mm(3) spatial resolution and a 6.5-sec frame rate was acquired on a 3T scanner. Undersampled data were reconstructed with a compressed sensing method without motion correction (FB-CS) and the proposed method (FB-LR). A follow-up respiratory-triggered acquisition (RT-CS) was performed as a reference standard. The reconstructed images were evaluated independently by two radiologists. Wilcoxon tests were performed to test the hypothesis that there was no significant difference between different reconstructions. Quantitative evaluation of contrast dynamics was also performed.The mean score of overall image quality of FB-LR was 4.0 on a 5-point scale, significantly better (P < 0.05) than FB-CS reconstruction (mean score 2.9), and similar to RT-CS (mean score 4.1). FB-LR also matched the temporal fidelity of contrast dynamics with a root mean square error less than 5%.Fast 3D free-breathing DCE MRI with high scan efficiency and image quality similar to respiratory-triggered acquisition is feasible in a pediatric clinical setting.J. Magn. Reson. Imaging 2013. © 2013 Wiley Periodicals, Inc.

  View details for DOI 10.1002/jmri.24551

  View details for PubMedID 24375859

• Accelerating Parameter Mapping with a Locally Low Rank Constraint MAGNETIC RESONANCE IN MEDICINE Zhang, T., Pauly, J. M., Levesque, I. R. 2015; 73 (2): 655-661

  Abstract

  To accelerate MR parameter mapping using a locally low rank (LLR) constraint, and the combination of parallel imaging and the LLR constraint.An LLR method is developed for MR parameter mapping and compared with a globally low rank method in a multiecho spin-echo T2 mapping experiment. For acquisition with coil arrays, a combined LLR and parallel imaging method is proposed. The proposed method is evaluated in a variable flip angle T1 mapping experiment and compared with the LLR method and parallel imaging alone.In the multiecho spin-echo T2 mapping experiment, the LLR method is more accurate than the globally low rank method for acceleration factors 2 and 3, especially for tissues with high T2 values. Variable flip angle T1 mapping is achieved by acquiring datasets with 10 flip angles, each dataset accelerated by a factor of 6, and reconstructed by the proposed method with a small normalized root mean square error of 0.025.The LLR method is likely superior to the globally low rank method for MR parameter mapping. The proposed combined LLR and parallel imaging method has better performance than the two methods alone, especially with highly accelerated acquisition. Magn Reson Med 73:655-661, 2015. © 2014 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.25161

  View details for Web of Science ID 000348139500022

  View details for PubMedID 24500817

  View details for PubMedCentralID PMC4122652

• Calibrationless Parallel Imaging Reconstruction Based on Structured Low-Rank Matrix Completion MAGNETIC RESONANCE IN MEDICINE Shin, P. J., Larson, P. E., Ohliger, M. A., Elad, M., Pauly, J. M., Vigneron, D. B., Lustig, M. 2014; 72 (4): 959-970

  Abstract

  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.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-onto-sets algorithm with singular value thresholding is described.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.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.

  View details for DOI 10.1002/mrm.24997

  View details for Web of Science ID 000342342300008

  View details for PubMedID 24248734

• Clinical performance of contrast enhanced abdominal pediatric MRI with fast combined parallel imaging compressed sensing reconstruction. Journal of magnetic resonance imaging : JMRI Zhang, T., Chowdhury, S., Lustig, M., Barth, R. A., Alley, M. T., Grafendorfer, T., Calderon, P. D., Robb, F. J., Pauly, J. M., Vasanawala, S. S. 2014; 40 (1): 13-25

  Abstract

  To deploy clinically, a combined parallel imaging compressed sensing method with coil compression that achieves a rapid image reconstruction, and assess its clinical performance in contrast-enhanced abdominal pediatric MRI.With Institutional Review Board approval and informed patient consent/assent, 29 consecutive pediatric patients were recruited. Dynamic contrast-enhanced MRI was acquired on a 3 Tesla scanner using a dedicated 32-channel pediatric coil and a three-dimensional SPGR sequence, with pseudo-random undersampling at a high acceleration (R = 7.2). Undersampled data were reconstructed with three methods: a traditional parallel imaging method and a combined parallel imaging compressed sensing method with and without coil compression. The three sets of images were evaluated independently and blindly by two radiologists at one siting, for overall image quality and delineation of anatomical structures. Wilcoxon tests were performed to test the hypothesis that there was no significant difference in the evaluations, and interobserver agreement was analyzed.Fast reconstruction with coil compression did not deteriorate image quality. The mean score of structural delineation of the fast reconstruction was 4.1 on a 5-point scale, significantly better (P < 0.05) than traditional parallel imaging (mean score 3.1). Fair to substantial interobserver agreement was reached in structural delineation assessment.A fast combined parallel imaging compressed sensing method is feasible in a pediatric clinical setting. Preliminary results suggest it may improve structural delineation over parallel imaging. J. Magn. Reson. Imaging 2014;40:13-25. © 2013 Wiley Periodicals, Inc.

  View details for DOI 10.1002/jmri.24333

  View details for PubMedID 24127123

  View details for PubMedCentralID PMC3984374

• Near-contiguous spin echo imaging using matched-phase RF and its application in velocity-selective arterial spin labeling. Magnetic resonance in medicine Zun, Z., Hargreaves, B. A., Pauly, J., Zaharchuk, G. 2014; 71 (6): 2043-2050

  Abstract

  The minimum slice spacing in multislice imaging is limited by inter-slice crosstalk due to an imperfect slice profile. This study sought to minimize the slice spacing using matched-phase RF pulses and demonstrate its application in cerebral blood flow imaging using velocity-selective arterial spin labeling.A spin-echo matched-phase 90°-180° RF pair was designed using Shinnar-Le Roux algorithm in order to improve the slice profile of longitudinal magnetization, which plays a more critical role in creating interslice crosstalk than transverse magnetization. Both transverse and longitudinal slice profiles were compared between matched-phase RF and sinc-based RF pulses in simulations and measurements. Velocity-selective arterial spin labeling was performed in normal volunteers using both RF pulses and standard deviation of cerebral blood flow time series was calculated to examine ASL signal stability.Using designed matched-phase RF, the longitudinal slice profile was sharpened without signal-to-noise ratio loss. In velocity-selective arterial spin labeling imaging, the temporal standard deviation of cerebral blood flow measurements was reduced from 48 mL/100 g/min to 32 mL/100 g/min by 33% using matched-phase RF pulses, and as a result, cerebral blood flow image quality improved.This study reports that near-contiguous multislice imaging can be achieved using matched-phase RF pulses without compromising signal-to-noise ratio and signal stability. Magn Reson Med, 2013. © 2013 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.24866

  View details for PubMedID 23857667

• Homogenous Fat Suppression for Bilateral Breast Imaging Using Independent Shims MAGNETIC RESONANCE IN MEDICINE Han, M., Cunningham, C. H., Pauly, J. M., Daniel, B. L., Hargreaves, B. A. 2014; 71 (4): 1511-1517

  Abstract

  To demonstrate the capability of incorporating independent shims into a dual-band spectral-spatial excitation and to compare fat suppression between standard global shims and independent shims for in vivo bilateral breast imaging at 1.5T.A dual-band spectral-spatial excitation pulse was designed by interleaving two flyback spectral-spatial pulses, playing one during positive gradient lobes and the other during negative gradient lobes. Each slab was enabled to have an independent spatial offset, spectral offset, and slab-phase modulation by modulating radiofrequency phase, and independent linear shims were incorporated by playing extra shim gradients. Phantom experiments were performed to demonstrate the functionality of the pulse, and in vivo experiments were performed for 10 healthy volunteers to compare fat suppression between standard shims and independent shims.The phantom experiments confirmed that the dual-band pulse can provide independent spectral and spatial offsets and linear shims to the two slabs. Independent shims provided qualitatively more homogeneous fat suppression than standard shims in seven out of 10 subjects, with equivalent fat suppression in two of the other three subjects.Incorporating independent shims into the dual-band spectral-spatial excitation can provide homogeneous fat suppression in bilateral breast imaging.

  View details for DOI 10.1002/mrm.24803

  View details for Web of Science ID 000333040500017

  View details for PubMedID 23821305

  View details for PubMedCentralID PMC4085331

• ESPIRiT-An Eigenvalue Approach to Autocalibrating Parallel MRI: Where SENSE Meets GRAPPA MAGNETIC RESONANCE IN MEDICINE Uecker, M., Lai, P., Murphy, M. J., Virtue, P., Elad, M., Pauly, J. M., Vasanawala, S. S., Lustig, M. 2014; 71 (3): 990-1001

  View details for DOI 10.1002/mrm.24751

  View details for Web of Science ID 000331614600011

• Improved Slice-Selective Adiabatic Excitation MAGNETIC RESONANCE IN MEDICINE Balchandani, P., Glover, G., Pauly, J., Spielman, D. 2014; 71 (1): 75-82

  Abstract

  PURPOSE: The purpose of this work is to design an improved Slice-selective Tunable-flip AdiaBatic Low peak-power Excitation (STABLE) pulse with shorter duration and increased off-resonance immunity to make it suitable for use in a greater range of applications and at higher field strengths. An additional aim is to design a variant of this pulse to achieve B(1) -insensitive, fat-suppressed excitation. METHODS: The adiabatic SLR algorithm was used to generate a more uniform spectral pulse envelope for this improved radiofrequency pulse for adiabatic slice-selective excitation, called STABLE-2. Pulse parameters were adjusted to design a version of STABLE-2 with a spectral null centered on lipids. RESULTS: In vivo images obtained of the human brain at 3 and 7 T demonstrate that STABLE-2 provides robust, uniform, slice-selective excitation over a range of B(1) values. Phantom and in vivo knee images obtained at 3 T demonstrate the effectiveness of STABLE-2 for fat suppression. CONCLUSIONS: STABLE-2 achieves B(1) -insensitive slice-selective excitation while providing greater off-resonance immunity and a shorter pulse duration, when compared to the original STABLE pulse. In particular, the 9.8-ms STABLE-2 pulse provides slice selectivity over 120 Hz whereas the 21-ms STABLE pulse is limited to 80 Hz off-resonance. B(1) -Insensitive fat-suppressed excitation may also be achieved by using a variant of this pulse. Magn Reson Med, 2013. © 2013 Wiley Periodicals, Inc.

  View details for DOI 10.1002/mrm.24630

  View details for Web of Science ID 000328580300010

  View details for PubMedID 23401184

• Quantitative Measurement of Cancer Metabolism Using Stimulated Echo Hyperpolarized Carbon-13 MRS MAGNETIC RESONANCE IN MEDICINE Swisher, C. L., Larson, P. E., Kruttwig, K., Kerr, A. B., Hu, S., Bok, R. A., Goga, A., Pauly, J. M., Nelson, S. J., Kurhanewicz, J., Vigneron, D. B. 2014; 71 (1): 1-11

  Abstract

  Magnetic resonance spectroscopy of hyperpolarized substrates allows for the observation of label exchange catalyzed by enzymes providing a powerful tool to investigate tissue metabolism and potentially kinetics in vivo. However, the accuracy of current methods to calculate kinetic parameters has been limited by T1 relaxation effects, extracellular signal contributions, and reduced precision at lower signal-to-noise ratio.To address these challenges, we investigated a new modeling technique using metabolic activity decomposition-stimulated echo acquisition mode. The metabolic activity decomposition-stimulated echo acquisition mode technique separates exchanging from nonexchanging metabolites providing twice the information as conventional techniques.This allowed for accurate measurements of rates of conversion and of multiple T1 values simultaneously using a single acquisition.The additional measurement of T1 values for the reaction metabolites provides further biological information about the cellular environment of the metabolites. The new technique was investigated through simulations and in vivo studies of transgenic mouse models of cancer demonstrating improved assessments of kinetic rate constants and new T1 relaxation value measurements for hyperpolarized (13) C-pyruvate, (13) C-lactate, and (13) C-alanine.

  View details for DOI 10.1002/mrm.24634

  View details for Web of Science ID 000328580300001

  View details for PubMedID 23412881

  View details for PubMedCentralID PMC3659200

• Optimal variable flip angle schemes for dynamic acquisition of exchanging hyperpolarized substrates JOURNAL OF MAGNETIC RESONANCE Xing, Y., Reed, G. D., Pauly, J. M., Kerr, A. B., Larson, P. E. 2013; 234: 75-81

  Abstract

  In metabolic MRI with hyperpolarized contrast agents, the signal levels vary over time due to T1 decay, T2 decay following RF excitations, and metabolic conversion. Efficient usage of the nonrenewable hyperpolarized magnetization requires specialized RF pulse schemes. In this work, we introduce two novel variable flip angle schemes for dynamic hyperpolarized MRI in which the flip angle is varied between excitations and between metabolites. These were optimized to distribute the magnetization relatively evenly throughout the acquisition by accounting for T1 decay, prior RF excitations, and metabolic conversion. Simulation results are presented to confirm the flip angle designs and evaluate the variability of signal dynamics across typical ranges of T1 and metabolic conversion. They were implemented using multiband spectral-spatial RF pulses to independently modulate the flip angle at various chemical shift frequencies. With these schemes we observed increased SNR of [1-(13)C]lactate generated from [1-(13)C]pyruvate, particularly at later time points. This will allow for improved characterization of tissue perfusion and metabolic profiles in dynamic hyperpolarized MRI.

  View details for DOI 10.1016/j.jmr.2013.06.003

  View details for Web of Science ID 000323085800009

  View details for PubMedID 23845910

  View details for PubMedCentralID PMC3765634

• Perfusion and diffusion sensitive C-13 stimulated-echo MRSI for metabolic imaging of cancer MAGNETIC RESONANCE IMAGING Larson, P. E., Hurd, R. E., Kerr, A. B., Pauly, J. M., Bok, R. A., Kurhanewicz, J., Vigneron, D. B. 2013; 31 (5): 635-642

  Abstract

  Metabolic imaging with hyperpolarized [1-(13)C]-pyruvate can rapidly probe tissue metabolic profiles in vivo and has been shown to provide cancer imaging biomarkers for tumor detection, progression, and response to therapy. This technique uses a bolus injection followed by imaging within 1-2 minutes. The observed metabolites include vascular components and their generation is also influenced by cellular transport. These factors complicate image interpretation, especially since [1-(13)C]lactate, a metabolic product that is a biomarker of cancer, is also produced by red blood cells. It would be valuable to understand the distribution of metabolites between the vasculature, interstitial space, and intracellular compartments. The purpose of this study was to better understand this compartmentalization by using a perfusion and diffusion-sensitive stimulated-echo acquisition mode (STEAM) MRSI acquisition method tailored to hyperpolarized substrates. Our results in mouse models showed that among metabolites, the injected substrate (13)C-pyruvate had the largest vascular fraction overall while (13)C-alanine had the smallest vascular fraction. We observed a larger vascular fraction of pyruvate and lactate in the kidneys and liver when compared to back muscle and prostate tumor tissue. Our data suggests that (13)C-lactate in prostate tumor tissue voxels was the most abundant labeled metabolite intracellularly. This was shown in STEAM images that highlighted abnormal cancer cell metabolism and suppressed vascular (13)C metabolite signals.

  View details for DOI 10.1016/j.mri.2012.10.020

  View details for Web of Science ID 000319103000001

  View details for PubMedID 23260391

  View details for PubMedCentralID PMC3626756

• Optimization of Transcutaneous Energy Transmission Systems Suitable for Left Ventricular Assist Devices JOURNAL OF MEDICAL DEVICES-TRANSACTIONS OF THE ASME Byron, K., Bluvshtein, V., Lucke, L., Pauly, J. 2013; 7 (2)

  View details for DOI 10.1115/1.4024432

  View details for Web of Science ID 000326117600041

• Coil compression for accelerated imaging with Cartesian sampling MAGNETIC RESONANCE IN MEDICINE Zhang, T., Pauly, J. M., Vasanawala, S. S., Lustig, M. 2013; 69 (2): 571-582

  Abstract

  MRI using receiver arrays with many coil elements can provide high signal-to-noise ratio and increase parallel imaging acceleration. At the same time, the growing number of elements results in larger datasets and more computation in the reconstruction. This is of particular concern in 3D acquisitions and in iterative reconstructions. Coil compression algorithms are effective in mitigating this problem by compressing data from many channels into fewer virtual coils. In Cartesian sampling there often are fully sampled k-space dimensions. In this work, a new coil compression technique for Cartesian sampling is presented that exploits the spatially varying coil sensitivities in these nonsubsampled dimensions for better compression and computation reduction. Instead of directly compressing in k-space, coil compression is performed separately for each spatial location along the fully sampled directions, followed by an additional alignment process that guarantees the smoothness of the virtual coil sensitivities. This important step provides compatibility with autocalibrating parallel imaging techniques. Its performance is not susceptible to artifacts caused by a tight imaging field-of-view. High quality compression of in vivo 3D data from a 32 channel pediatric coil into six virtual coils is demonstrated.

  View details for DOI 10.1002/mrm.24267

  View details for Web of Science ID 000314059500031

  View details for PubMedID 22488589

  View details for PubMedCentralID PMC3396763

• A rapid method for direct detection of metabolic conversion and magnetization exchange with application to hyperpolarized substrates JOURNAL OF MAGNETIC RESONANCE Larson, P. E., Kerr, A. B., Swisher, C. L., Pauly, J. M., Vigneron, D. B. 2012; 225: 71-80

  Abstract

  In this work, we present a new MR spectroscopy approach for directly observing nuclear spins that undergo exchange, metabolic conversion, or, generally, any frequency shift during a mixing time. Unlike conventional approaches to observe these processes, such as exchange spectroscopy (EXSY), this rapid approach requires only a single encoding step and thus is readily applicable to hyperpolarized MR in which the magnetization is not replenished after T(1) decay and RF excitations. This method is based on stimulated-echoes and uses phase-sensitive detection in conjunction with precisely chosen echo times in order to separate spins generated during the mixing time from those present prior to mixing. We are calling the method Metabolic Activity Decomposition Stimulated-echo Acquisition Mode or MAD-STEAM. We have validated this approach as well as applied it in vivo to normal mice and a transgenic prostate cancer mouse model for observing pyruvate-lactate conversion, which has been shown to be elevated in numerous tumor types. In this application, it provides an improved measure of cellular metabolism by separating [1-(13)C]-lactate produced in tissue by metabolic conversion from [1-(13)C]-lactate that has flowed into the tissue or is in the blood. Generally, MAD-STEAM can be applied to any system in which spins undergo a frequency shift.

  View details for DOI 10.1016/j.jmr.2012.09.014

  View details for Web of Science ID 000312051700011

  View details for PubMedID 23143011

  View details for PubMedCentralID PMC3531583

• Nonrigid motion correction in 3D using autofocusing withlocalized linear translations MAGNETIC RESONANCE IN MEDICINE Cheng, J. Y., Alley, M. T., Cunningham, C. H., Vasanawala, S. S., Pauly, J. M., Lustig, M. 2012; 68 (6): 1785-1797

  Abstract

  MR scans are sensitive to motion effects due to the scan duration. To properly suppress artifacts from nonrigid body motion, complex models with elements such as translation, rotation, shear, and scaling have been incorporated into the reconstruction pipeline. However, these techniques are computationally intensive and difficult to implement for online reconstruction. On a sufficiently small spatial scale, the different types of motion can be well approximated as simple linear translations. This formulation allows for a practical autofocusing algorithm that locally minimizes a given motion metric--more specifically, the proposed localized gradient-entropy metric. To reduce the vast search space for an optimal solution, possible motion paths are limited to the motion measured from multichannel navigator data. The novel navigation strategy is based on the so-called "Butterfly" navigators, which are modifications of the spin-warp sequence that provides intrinsic translational motion information with negligible overhead. With a 32-channel abdominal coil, sufficient number of motion measurements were found to approximate possible linear motion paths for every image voxel. The correction scheme was applied to free-breathing abdominal patient studies. In these scans, a reduction in artifacts from complex, nonrigid motion was observed.

  View details for DOI 10.1002/mrm.24189

  View details for Web of Science ID 000311398600012

  View details for PubMedID 22307933

  View details for PubMedCentralID PMC3376676

• Reducing artifacts in one-dimensional Fourier velocity encoding for fast and pulsatile flow MAGNETIC RESONANCE IN MEDICINE Lee, D., Santos, J. M., Hu, B. S., Pauly, J. M., Kerr, A. B. 2012; 68 (6): 1876-1885

  Abstract

  When evaluating the severity of valvular stenosis, the peak velocity of the blood flow is routinely used to estimate the transvalvular pressure gradient. One-dimensional Fourier velocity encoding effectively detects the peak velocity with an ungated time series of spatially resolved velocity spectra in real time. However, measurement accuracy can be degraded by the pulsatile and turbulent nature of stenotic flow and the existence of spatially varying off-resonance. In this work, we investigate the feasibility of improving the peak velocity detection capability of one-dimensional Fourier velocity encoding for stenotic flow using a novel echo-shifted interleaved readout combined with a variable-density circular k-space trajectory. The shorter echo and readout times of the echo-shifted interleaved acquisitions are designed to reduce sensitivity to off-resonance. Preliminary results from limited phantom and in vivo results also indicate that some artifacts from pulsatile flow appear to be suppressed when using this trajectory compared to conventional single-shot readouts, suggesting that peak velocity detection may be improved. The efficiency of the new trajectory improves the temporal and spatial resolutions. To realize the proposed readout, a novel multipoint-traversing algorithm is introduced for flexible and automated gradient-waveform design.

  View details for DOI 10.1002/mrm.24212

  View details for Web of Science ID 000311398600021

  View details for PubMedID 22457248

  View details for PubMedCentralID PMC3499673

• Self-Refocused Adiabatic Pulse for Spin Echo Imaging at 7 T MAGNETIC RESONANCE IN MEDICINE Balchandani, P., Khalighi, M. M., Glover, G., Pauly, J., Spielman, D. 2012; 67 (4): 1077-1085

  Abstract

  Spin echo pulse sequences are used to produce clinically important T(2) contrast. However, conventional 180° radiofrequency pulses required to generate a spin echo are highly susceptible to the B(1) inhomogeneity at high magnetic fields such as 7 Tesla (7 T), resulting in varying signal and contrast over the region of interest. Adiabatic 180° pulses may be used to replace conventional 180° pulses in spin echo sequences to provide greater immunity to the inhomogeneous B(1) field at 7 T. However, because the spectral profile of an adiabatic 180° pulse has nonlinear phase, pairs of these pulses are needed for proper refocusing, resulting in increased radiofrequency power deposition and long minimum echo times. We used the adiabatic Shinnar Le-Roux method to generate a matched-phase adiabatic 90°-180° pulse pair to obviate the need for a second adiabatic 180° pulse for phase refocusing. The pulse pair was then reformulated into a single self-refocused pulse to minimize the echo time, and phantom and in vivo experiments were performed to validate pulse performance. The self-refocused adiabatic pulse produced transmit profiles that were substantially more uniform than those achieved using a conventional spin echo sequence.

  View details for DOI 10.1002/mrm.23089

  View details for Web of Science ID 000301533500021

  View details for PubMedID 21954048

  View details for PubMedCentralID PMC3548423

• RF Field Visualization of RF Ablation at the Larmor Frequency IEEE TRANSACTIONS ON MEDICAL IMAGING Shultz, K., Stang, P., Kerr, A., Pauly, J., Scott, G. 2012; 31 (4): 938-947

  Abstract

  Radio-frequency ablation (RFA) is an effective minimally invasive treatment for tumors. One primary source of difficulty is monitoring and controlling the ablation region. Currently, RFA is performed at 460 kHz, for which magnetic resonance imaging (MRI) could play a role given its capability for temperature monitoring and tumor visualization. If instead the ablation were to be performed at the MRI Larmor frequency, then the MR capability for B(1) field mapping could be used to directly visualize the radio-frequency (RF) fields created by the ablation currents. Visualizing the RF fields may enable better control of the ablation currents, enabling better control of lesion shape and size and improving repeatability. We demonstrate the feasibility of performing RFAs at 64 MHz and show preliminary results from imaging the RF fields from the ablation. The post-ablation RF fields show an increase in current density in the ablated region, consistent with an increase in conductivity of the ablated tissue.

  View details for DOI 10.1109/TMI.2011.2162248

  View details for Web of Science ID 000302547400008

  View details for PubMedID 21775256

  View details for PubMedCentralID PMC3321073

• A method for simultaneous echo planar imaging of hyperpolarized C-13 pyruvate and C-13 lactate JOURNAL OF MAGNETIC RESONANCE Reed, G. D., Larson, P. E., Von Morze, C., Bok, R., Lustig, M., Kerr, A. B., Pauly, J. M., Kurhanewicz, J., Vigneron, D. B. 2012; 217: 41-47

  Abstract

  A rapid echo planar imaging sequence for dynamic imaging of [1-(13)C] lactate and [1-(13)C] pyruvate simultaneously was developed. Frequency-based separation of these metabolites was achieved by spatial shifting in the phase-encoded direction with the appropriate choice of echo spacing. Suppression of the pyruvate-hydrate and alanine resonances is achieved through an optimized spectral-spatial RF waveform. Signal sampling efficiency as a function of pyruvate and lactate excitation angle was simulated using two site exchange models. Dynamic imaging is demonstrated in a transgenic mouse model, and phantom validations of the RF pulse frequency selectivity were performed.

  View details for DOI 10.1016/j.jmr.2012.02.008

  View details for Web of Science ID 000303083500007

  View details for PubMedID 22405760

  View details for PubMedCentralID PMC3326401

• Analysis of the BOLD characteristics in pass-band bSSFP fMRI INTERNATIONAL JOURNAL OF IMAGING SYSTEMS AND TECHNOLOGY Kim, T. S., Lee, J., Lee, J. H., Glover, G. H., Pauly, J. M. 2012; 22 (1): 23-32

  Abstract

  Balanced steady-state free precession (bSSFP) has been proposed as an alternative method to acquire the blood oxygenation level dependent contrast. Particularly, pass-band bSSFP functional magnetic resonance imaging (fMRI) is believed to utilize the T2 sensitivity of bSSFP in a relatively wide and flat off-resonance frequency band of the bSSFP profile. The method has a potential to provide higher signal to noise ratio (SNR) efficiency with reduced imaging artifacts compared to conventional approaches. Previous experimental results suggested that the level of the functional contrast and its characteristics are significantly influenced by the sequence parameters. However, few of these contrast characteristics have been investigated systematically. In this study, a computer simulation was performed to investigate the sources of functional contrast and the influence of scan parameters on the functional contrast to elucidate the contrast characteristics of pass-band bSSFP fMRI. Experiments were performed to validate the simulation results.

  View details for DOI 10.1002/ima.21296

  View details for Web of Science ID 000300505200004

  View details for PubMedCentralID PMC3646401

• Analysis of the BOLD Characteristics in Pass-Band bSSFP fMRI. International journal of imaging systems and technology Kim, T. S., Lee, J., Lee, J. H., Glover, G. H., Pauly, J. M. 2012; 22 (1): 23-32

  Abstract

  Balanced steady-state free precession (bSSFP) has been proposed as an alternative method to acquire the blood oxygenation level dependent contrast. Particularly, pass-band bSSFP functional magnetic resonance imaging (fMRI) is believed to utilize the T2 sensitivity of bSSFP in a relatively wide and flat off-resonance frequency band of the bSSFP profile. The method has a potential to provide higher signal to noise ratio (SNR) efficiency with reduced imaging artifacts compared to conventional approaches. Previous experimental results suggested that the level of the functional contrast and its characteristics are significantly influenced by the sequence parameters. However, few of these contrast characteristics have been investigated systematically. In this study, a computer simulation was performed to investigate the sources of functional contrast and the influence of scan parameters on the functional contrast to elucidate the contrast characteristics of pass-band bSSFP fMRI. Experiments were performed to validate the simulation results.

  View details for DOI 10.1002/ima.21296

  View details for PubMedID 23661904

  View details for PubMedCentralID PMC3646401

• Medusa: A Scalable MR Console Using USB IEEE TRANSACTIONS ON MEDICAL IMAGING Stang, P. P., Conolly, S. M., Santos, J. M., Pauly, J. M., Scott, G. C. 2012; 31 (2): 370-379

  Abstract

  Magnetic resonance imaging (MRI) pulse sequence consoles typically employ closed proprietary hardware, software, and interfaces, making difficult any adaptation for innovative experimental technology. Yet MRI systems research is trending to higher channel count receivers, transmitters, gradient/shims, and unique interfaces for interventional applications. Customized console designs are now feasible for researchers with modern electronic components, but high data rates, synchronization, scalability, and cost present important challenges. Implementing large multichannel MR systems with efficiency and flexibility requires a scalable modular architecture. With Medusa, we propose an open system architecture using the universal serial bus (USB) for scalability, combined with distributed processing and buffering to address the high data rates and strict synchronization required by multichannel MRI. Medusa uses a modular design concept based on digital synthesizer, receiver, and gradient blocks, in conjunction with fast programmable logic for sampling and synchronization. Medusa is a form of synthetic instrument, being reconfigurable for a variety of medical/scientific instrumentation needs. The Medusa distributed architecture, scalability, and data bandwidth limits are presented, and its flexibility is demonstrated in a variety of novel MRI applications.

  View details for DOI 10.1109/TMI.2011.2169681

  View details for Web of Science ID 000300197500018

  View details for PubMedID 21954200

  View details for PubMedCentralID PMC3282593

• Generating Super Stimulated-Echoes in MRI and Their Application to Hyperpolarized C-13 Diffusion Metabolic Imaging IEEE TRANSACTIONS ON MEDICAL IMAGING Larson, P. E., Kerr, A. B., Reed, G. D., Hurd, R. E., Kurhanewicz, J., Pauly, J. M., Vigneron, D. B. 2012; 31 (2): 265-275

  Abstract

  Stimulated-echoes in MR can be used to provide high sensitivity to motion and flow, creating diffusion and perfusion weighting as well as T(1) contrast, but conventional approaches inherently suffer from a 50% signal loss. The super stimulated-echo, which uses a specialized radio-frequency (RF) pulse train, has been proposed in order to improve the signal while preserving motion and T(1) sensitivity. This paper presents a novel and straightforward method for designing the super stimulated-echo pulse train using inversion pulse design techniques. This method can also create adiabatic designs with an improved response to RF transmit field variations. The scheme was validated in phantom experiments and shown in vivo to improve signal-to-noise ratio (SNR). We have applied a super stimulated-echo to metabolic MRI with hyperpolarized (13)C-labeled molecules. For spectroscopic imaging of hyperpolarized agents, several repetition times are required but only a single stimulated-echo encoding is feasible, which can lead to unwanted motion blurring. To address this, a super stimulated-echo preparation scheme was used in which the diffusion weighting is terminated prior to the acquisition, and we observed a SNR increases of 60% in phantoms and 49% in vivo over a conventional stimulated-echo. Experiments following injection of hyperpolarized [1-(13)C] -pyruvate in murine transgenic cancer models have shown improved delineation for tumors since signals from metabolites within tumor tissues are retained while those from the vasculature are suppressed by the diffusion preparation scheme.

  View details for DOI 10.1109/TMI.2011.2168235

  View details for Web of Science ID 000300197500010

  View details for PubMedID 22027366

  View details for PubMedCentralID PMC3274664

• A k-space analysis of small-tip-angle excitation. 1989. Journal of magnetic resonance Pauly, J., Nishimura, D., Macovski, A. 2011; 213 (2): 544-557

  View details for DOI 10.1016/j.jmr.2011.09.023

  View details for PubMedID 22152370

• Introduction to: A k-space analysis of small-tip-angle excitation. Journal of magnetic resonance Pauly, J. M., Nishimura, D. G., Macovski, A. 2011; 213 (2): 558-559

  Abstract

  The article "A k-space analysis of small-tip-angle excitation" introduced a spatial frequency interpretation of the effect of RF excitation pulses. This introduction describes where the initial ideas for this paper came from, and traces out some of the applications that have been developed using this perspective.

  View details for DOI 10.1016/j.jmr.2011.08.008

  View details for PubMedID 21890389

• Response to Comments on "Ensuring Safety of Implanted Devices Under MRI Using Reversed RF Polarization" MAGNETIC RESONANCE IN MEDICINE Overall, W. R., Pauly, J. M., Stang, P. P., Scott, G. C. 2011; 66 (6): 1517-1517

  View details for DOI 10.1002/mrm.23183

  View details for Web of Science ID 000297285000004

• Cross-relaxation Imaging of Human Articular Cartilage MAGNETIC RESONANCE IN MEDICINE Stikov, N., Keenan, K. E., Pauly, J. M., Smith, R. L., Dougherty, R. F., Gold, G. E. 2011; 66 (3): 725-734

  Abstract

  In this article, cross-relaxation imaging is applied to human ex vivo knee cartilage, and correlations of the cross-relaxation imaging parameters with macromolecular content in articular cartilage are reported. We show that, unlike the more commonly used magnetization transfer ratio, the bound pool fraction, the cross-relaxation rate (k) and the longitudinal relaxation time (T(1)) vary with depth and can therefore provide insight into the differences between the top and bottom layers of articular cartilage. Our cross-relaxation imaging model is more sensitive to macromolecular content in the top layers of cartilage, with bound pool fraction showing moderate correlations with proteoglycan content, and k and T(1) exhibiting moderate correlations with collagen.

  View details for DOI 10.1002/mrm.22865

  View details for Web of Science ID 000293988000013

  View details for PubMedID 21416504

  View details for PubMedCentralID PMC3130884

• Metal-Induced Artifacts in MRI AMERICAN JOURNAL OF ROENTGENOLOGY Hargreaves, B. A., Worters, P. W., Pauly, K. B., Pauly, J. M., Koch, K. M., Gold, G. E. 2011; 197 (3): 547-555

  Abstract

  The purpose of this article is to review some of the basic principles of imaging and how metal-induced susceptibility artifacts originate in MR images. We will describe common ways to reduce or modify artifacts using readily available imaging techniques, and we will discuss some advanced methods to correct readout-direction and slice-direction artifacts.The presence of metallic implants in MRI can cause substantial image artifacts, including signal loss, failure of fat suppression, geometric distortion, and bright pile-up artifacts. These cause large resonant frequency changes and failure of many MRI mechanisms. Careful parameter and pulse sequence selections can avoid or reduce artifacts, although more advanced imaging methods offer further imaging improvements.

  View details for DOI 10.2214/AJR.11.7364

  View details for Web of Science ID 000294165600037

  View details for PubMedID 21862795

• Fast Concomitant Gradient Field and Field Inhomogeneity Correction for Spiral Cardiac Imaging MAGNETIC RESONANCE IN MEDICINE Cheng, J. Y., Santos, J. M., Pauly, J. M. 2011; 66 (2): 390-401

  Abstract

  Non-Cartesian imaging provides many advantages in terms of flexibility, functionality, and speed. However, a major drawback to these imaging methods is off-resonance distortion artifacts. These artifacts manifest as blurring in spiral imaging. Common techniques that remove the off-resonance field inhomogeneity distortion effects are not sufficient, because the high order concomitant gradient fields are nontrivial for common imaging conditions, such as imaging 5 cm off isocenter in an 1.5 T scanner. Previous correction algorithms are either slow or do not take into account the known effects of concomitant gradient fields along with the field inhomogeneities. To ease the correction, the distortion effects are modeled as a non-stationary convolution problem. In this work, two fast and accurate postgridding algorithms are presented and analyzed. These methods account for both the concomitant field effects and the field inhomogeneities. One algorithm operates in the frequency domain and the other in the spatial domain. To take advantage of their speed and accuracy, the algorithms are applied to a real-time cardiac study and a high-resolution cardiac study. Both of the presented algorithms provide for a practical solution to the off-resonance problem in spiral imaging.

  View details for DOI 10.1002/mrm.22802

  View details for Web of Science ID 000293256800010

  View details for PubMedID 21384423

  View details for PubMedCentralID PMC3158031

• Slice Encoding for Metal Artifact Correction With Noise Reduction MAGNETIC RESONANCE IN MEDICINE Lu, W., Pauly, K. B., Gold, G. E., Pauly, J. M., Hargreaves, B. A. 2011; 65 (5): 1352-1357

  Abstract

  Magnetic resonance imaging (MRI) near metallic implants is often hampered by severe metal artifacts. To obtain distortion-free MR images near metallic implants, SEMAC (Slice Encoding for Metal Artifact Correction) corrects metal artifacts via robust encoding of excited slices against metal-induced field inhomogeneities, followed by combining the data resolved from multiple SEMAC-encoded slices. However, as many of the resolved data elements only contain noise, SEMAC-corrected images can suffer from relatively low signal-to-noise ratio. Improving the signal-to-noise ratio of SEMAC-corrected images is essential to enable SEMAC in routine clinical studies. In this work, a new reconstruction procedure is proposed to reduce noise in SEMAC-corrected images. A singular value decomposition denoising step is first applied to suppress quadrature noise in multi-coil SEMAC-encoded slices. Subsequently, the singular value decomposition-denoised data are selectively included in the correction of through-plane distortions. The experimental results demonstrate that the proposed reconstruction procedure significantly improves the SNR without compromising the correction of metal artifacts.

  View details for DOI 10.1002/mrm.22796

  View details for Web of Science ID 000289760800018

  View details for PubMedID 21287596

  View details for PubMedCentralID PMC3079010

• Fast Dynamic 3D MR Spectroscopic Imaging With Compressed Sensing and Multiband Excitation Pulses for Hyperpolarized C-13 Studies MAGNETIC RESONANCE IN MEDICINE Larson, P. E., Hu, S., Lustig, M., Kerr, A. B., Nelson, S. J., Kurhanewicz, J., Pauly, J. M., Vigneron, D. B. 2011; 65 (3): 610-619

  Abstract

  Hyperpolarized 13C MR spectroscopic imaging can detect not only the uptake of the pre-polarized molecule but also its metabolic products in vivo, thus providing a powerful new method to study cellular metabolism. Imaging the dynamic perfusion and conversion of these metabolites provides additional tissue information but requires methods for efficient hyperpolarization usage and rapid acquisitions. In this work, we have developed a time-resolved 3D MR spectroscopic imaging method for acquiring hyperpolarized 13C data by combining compressed sensing methods for acceleration and multiband excitation pulses to efficiently use the magnetization. This method achieved a 2 sec temporal resolution with full volumetric coverage of a mouse, and metabolites were observed for up to 60 sec following injection of hyperpolarized [1-(13)C]-pyruvate. The compressed sensing acquisition used random phase encode gradient blips to create a novel random undersampling pattern tailored to dynamic MR spectroscopic imaging with sampling incoherency in four (time, frequency, and two spatial) dimensions. The reconstruction was also tailored to dynamic MR spectroscopic imaging by applying a temporal wavelet sparsifying transform to exploit the inherent temporal sparsity. Customized multiband excitation pulses were designed with a lower flip angle for the [1-(13)C]-pyruvate substrate given its higher concentration than its metabolic products ([1-(13)C]-lactate and [1-(13)C]-alanine), thus using less hyperpolarization per excitation. This approach has enabled the monitoring of perfusion and uptake of the pyruvate, and the conversion dynamics to lactate and alanine throughout a volume with high spatial and temporal resolution.

  View details for DOI 10.1002/mrm.22650

  View details for Web of Science ID 000287929800002

  View details for PubMedID 20939089

  View details for PubMedCentralID PMC3021589

• Frequency-Offset Cartesian Feedback for MRI Power Amplifier Linearization IEEE TRANSACTIONS ON MEDICAL IMAGING Zanchi, M. G., Stang, P., Kerr, A., Pauly, J. M., Scott, G. C. 2011; 30 (2): 512-522

  Abstract

  High-quality magnetic resonance imaging (MRI) requires precise control of the transmit radio-frequency (RF) field. In parallel excitation applications such as transmit SENSE, high RF power linearity is essential to cancel aliased excitations. In widely-employed class AB power amplifiers, gain compression, cross-over distortion, memory effects, and thermal drift all distort the RF field modulation and can degrade image quality. Cartesian feedback (CF) linearization can mitigate these effects in MRI, if the quadrature mismatch and dc offset imperfections inherent in the architecture can be minimized. In this paper, we present a modified Cartesian feedback technique called "frequency-offset Cartesian feedback" (FOCF) that significantly reduces these problems. In the FOCF architecture, the feedback control is performed at a low intermediate frequency rather than dc, so that quadrature ghosts and dc errors are shifted outside the control bandwidth. FOCF linearization is demonstrated with a variety of typical MRI pulses. Simulation of the magnetization obtained with the Bloch equation demonstrates that high-fidelity RF reproduction can be obtained even with inexpensive class AB amplifiers. Finally, the enhanced RF fidelity of FOCF over CF is demonstrated with actual images obtained in a 1.5 T MRI system.

  View details for DOI 10.1109/TMI.2010.2087768

  View details for Web of Science ID 000286931000029

  View details for PubMedID 20959264

  View details for PubMedCentralID PMC3155726

• Prediction of glycosaminoglycan content in human cartilage by age, T1 rho and T2 MRI OSTEOARTHRITIS AND CARTILAGE Keenan, K. E., Besier, T. F., Pauly, J. M., Han, E., Rosenberg, J., Smith, R. L., Delp, S. L., Beaupre, G. S., Gold, G. E. 2011; 19 (2): 171-179

  Abstract

  A relationship between T1ρ relaxation time and glycosaminoglycan (GAG) content has been demonstrated in chemically degraded bovine cartilage, but has not been demonstrated with quantitative biochemistry in human cartilage. A relationship has also been established between T2 relaxation time in cartilage and osteoarthritis (OA) severity. We hypothesized that T1ρ relaxation time would be associated with GAG content in human cartilage with normal T2 relaxation times.T2 relaxation time, T1ρ relaxation time, and glycosaminoglycan as a percentage of wet weight (sGAG) were measured for top and bottom regions at 7 anatomical locations in 21 human cadaver patellae. For our analysis, T2 relaxation time was classified as normal or elevated based on a threshold defined by the mean plus one standard deviation of the T2 relaxation time for all samples.In the normal T2 relaxation time subset, T1ρ relaxation time correlated with sGAG content in the full-thickness and bottom regions, but only marginally in the top region alone. sGAG content decreased significantly with age in all regions.In the subset of cartilage specimens with normal T2 relaxation time, T1ρ relaxation time was inversely associated with sGAG content, as hypothesized. A predictive model, which accounts for T2 relaxation time and the effects of age, might be able to determine longitudinal trends in GAG content in the same person based on T1ρ relaxation time maps.

  View details for DOI 10.1016/j.joca.2010.11.009

  View details for Web of Science ID 000287470600005

  View details for PubMedID 21112409

  View details for PubMedCentralID PMC3041640

• Bound pool fractions complement diffusion measures to describe white matter micro and macrostructure NEUROIMAGE Stikov, N., Perry, L. M., Mezer, A., Rykhlevskaia, E., Wandell, B. A., Pauly, J. M., Dougherty, R. F. 2011; 54 (2): 1112-1121

  Abstract

  Diffusion imaging and bound pool fraction (BPF) mapping are two quantitative magnetic resonance imaging techniques that measure microstructural features of the white matter of the brain. Diffusion imaging provides a quantitative measure of the diffusivity of water in tissue. BPF mapping is a quantitative magnetization transfer (qMT) technique that estimates the proportion of exchanging protons bound to macromolecules, such as those found in myelin, and is thus a more direct measure of myelin content than diffusion. In this work, we combined BPF estimates of macromolecular content with measurements of diffusivity within human white matter tracts. Within the white matter, the correlation between BPFs and diffusivity measures such as fractional anisotropy and radial diffusivity was modest, suggesting that diffusion tensor imaging and bound pool fractions are complementary techniques. We found that several major tracts have high BPF, suggesting a higher density of myelin in these tracts. We interpret these results in the context of a quantitative tissue model.

  View details for DOI 10.1016/j.neuroimage.2010.08.068

  View details for Web of Science ID 000285486000036

  View details for PubMedID 20828622

  View details for PubMedCentralID PMC2997845

• PRACTICAL PARALLEL IMAGING COMPRESSED SENSING MRI: SUMMARY OF TWO YEARS OF EXPERIENCE IN ACCELERATING BODY MRI OF PEDIATRIC PATIENTS. 8th IEEE International Symposium on Biomedical Imaging (ISBI) - From Nano to Macro Vasanawala, S. S., MURPHY, M. J., Alley, M. T., Lai, P., Keutzer, K., Pauly, J. M., Lustig, M. IEEE. 2011: 1039–1043

  View details for Web of Science ID 000298849400238

• Compressed Sensing for Chemical Shift-Based Water-Fat Separation MAGNETIC RESONANCE IN MEDICINE Doneva, M., Boernert, P., Eggers, H., Mertins, A., Pauly, J., Lustig, M. 2010; 64 (6): 1749-1759

  Abstract

  Multi echo chemical shift-based water-fat separation methods allow for uniform fat suppression in the presence of main field inhomogeneities. However, these methods require additional scan time for chemical shift encoding. This work presents a method for water-fat separation from undersampled data (CS-WF), which combines compressed sensing and chemical shift-based water-fat separation. Undersampling was applied in the k-space and in the chemical shift encoding dimension to reduce the total scanning time. The method can reconstruct high quality water and fat images in 2D and 3D applications from undersampled data. As an extension, multipeak fat spectral models were incorporated into the CS-WF reconstruction to improve the water-fat separation quality. In 3D MRI, reduction factors of above three can be achieved, thus fully compensating the additional time needed in three-echo water-fat imaging. The method is demonstrated on knee and abdominal in vivo data.

  View details for DOI 10.1002/mrm.22563

  View details for Web of Science ID 000284659300025

  View details for PubMedID 20859998

• Minimum Envelope Roughness Pulse Design for Reduced Amplifier Distortion in Parallel Excitation MAGNETIC RESONANCE IN MEDICINE Grissom, W. A., Kerr, A. B., Stang, P., Scott, G. C., Pauly, J. M. 2010; 64 (5): 1433-1440

  Abstract

  Parallel excitation uses multiple transmit channels and coils, each driven by independent waveforms, to afford the pulse designer an additional spatial encoding mechanism that complements gradient encoding. In contrast to parallel reception, parallel excitation requires individual power amplifiers for each transmit channel, which can be cost prohibitive. Several groups have explored the use of low-cost power amplifiers for parallel excitation; however, such amplifiers commonly exhibit nonlinear memory effects that distort radio frequency pulses. This is especially true for pulses with rapidly varying envelopes, which are common in parallel excitation. To overcome this problem, we introduce a technique for parallel excitation pulse design that yields pulses with smoother envelopes. We demonstrate experimentally that pulses designed with the new technique suffer less amplifier distortion than unregularized pulses and pulses designed with conventional regularization.

  View details for DOI 10.1002/mrm.22512

  View details for Web of Science ID 000283616900023

  View details for PubMedCentralID PMC3053148

• Minimum envelope roughness pulse design for reduced amplifier distortion in parallel excitation. Magnetic resonance in medicine Grissom, W. A., Kerr, A. B., Stang, P., Scott, G. C., Pauly, J. M. 2010; 64 (5): 1432-1439

  Abstract

  Parallel excitation uses multiple transmit channels and coils, each driven by independent waveforms, to afford the pulse designer an additional spatial encoding mechanism that complements gradient encoding. In contrast to parallel reception, parallel excitation requires individual power amplifiers for each transmit channel, which can be cost prohibitive. Several groups have explored the use of low-cost power amplifiers for parallel excitation; however, such amplifiers commonly exhibit nonlinear memory effects that distort radio frequency pulses. This is especially true for pulses with rapidly varying envelopes, which are common in parallel excitation. To overcome this problem, we introduce a technique for parallel excitation pulse design that yields pulses with smoother envelopes. We demonstrate experimentally that pulses designed with the new technique suffer less amplifier distortion than unregularized pulses and pulses designed with conventional regularization.

  View details for DOI 10.1002/mrm.22512

  View details for PubMedID 20632401

  View details for PubMedCentralID PMC3053148

• Reweighted l(1) Referenceless PRF Shift Thermometry MAGNETIC RESONANCE IN MEDICINE Grissom, W. A., Lustig, M., Holbrook, A. B., Rieke, V., Pauly, J. M., Butts-Pauly, K. 2010; 64 (4): 1068-1077

  Abstract

  Temperature estimation in proton resonance frequency (PRF) shift MR thermometry requires a reference, or pretreatment, phase image that is subtracted from image phase during thermal treatment to yield a phase difference image proportional to temperature change. Referenceless thermometry methods derive a reference phase image from the treatment image itself by assuming that in the absence of a hot spot, the image phase can be accurately represented in a smooth (usually low order polynomial) basis. By masking the hot spot out of a least squares (ℓ(2)) regression, the reference phase image's coefficients on the polynomial basis are estimated and a reference image is derived by evaluating the polynomial inside the hot spot area. Referenceless methods are therefore insensitive to motion and bulk main field shifts, however, currently these methods require user interaction or sophisticated tracking to ensure that the hot spot is masked out of the polynomial regression. This article introduces an approach to reference PRF shift thermometry that uses reweighted ℓ(1) regression, a form of robust regression, to obtain background phase coefficients without hot spot tracking and masking. The method is compared to conventional referenceless thermometry, and demonstrated experimentally in monitoring HIFU heating in a phantom and canine prostate, as well as in a healthy human liver.

  View details for DOI 10.1002/mrm.22502

  View details for Web of Science ID 000282477100015

  View details for PubMedID 20564600

  View details for PubMedCentralID PMC3155729

• Designing Adiabatic Radio Frequency Pulses Using the Shinnar-Le Roux Algorithm MAGNETIC RESONANCE IN MEDICINE Balchandani, P., Pauly, J., Spielman, D. 2010; 64 (3): 843-851

  Abstract

  Adiabatic pulses are a special class of radio frequency (RF) pulses that may be used to achieve uniform flip angles in the presence of a nonuniform B(1) field. In this work, we present a new, systematic method for designing high-bandwidth (BW), low-peak-amplitude adiabatic RF pulses that utilizes the Shinnar-Le Roux (SLR) algorithm for pulse design. Currently, the SLR algorithm is extensively employed to design nonadiabatic pulses for use in magnetic resonance imaging and spectroscopy. We have adapted the SLR algorithm to create RF pulses that also satisfy the adiabatic condition. By overlaying sufficient quadratic phase across the spectral profile before the inverse SLR transform, we generate RF pulses that exhibit the required spectral characteristics and adiabatic behavior. Application of quadratic phase also distributes the RF energy more uniformly, making it possible to obtain the same spectral BW with lower RF peak amplitude. The method enables the pulse designer to specify spectral profile parameters and the degree of quadratic phase before pulse generation. Simulations and phantom experiments demonstrate that RF pulses designed using this new method behave adiabatically.

  View details for DOI 10.1002/mrm.22473

  View details for Web of Science ID 000281346300025

  View details for PubMedID 20806378

  View details for PubMedCentralID PMC2975518

• Ensuring Safety of Implanted Devices Under MRI Using Reversed RF Polarization MAGNETIC RESONANCE IN MEDICINE Overall, W. R., Pauly, J. M., Stang, P. P., Scott, G. C. 2010; 64 (3): 823-833

  Abstract

  Patients with long-wire medical implants are currently prevented from undergoing magnetic resonance imaging (MRI) scans due to the risk of radio frequency (RF) heating. We have developed a simple technique for determining the heating potential for these implants using reversed radio frequency (RF) polarization. This technique could be used on a patient-to-patient basis as a part of the standard prescan procedure to ensure that the subject's device does not pose a heating risk. By using reversed quadrature polarization, the MR scan can be sensitized exclusively to the potentially dangerous currents in the device. Here, we derive the physical principles governing the technique and explore the primary sources of inaccuracy. These principles are verified through finite-difference simulations and through phantom scans of implant leads. These studies demonstrate the potential of the technique for sensitively detecting potentially dangerous coupling conditions before they can do any harm.

  View details for DOI 10.1002/mrm.22468

  View details for Web of Science ID 000281346300023

  View details for PubMedID 20593374

  View details for PubMedCentralID PMC3053145

• Improved Pediatric MR Imaging with Compressed Sensing RADIOLOGY Vasanawala, S. S., Alley, M. T., Hargreaves, B. A., Barth, R. A., Pauly, J. M., Lustig, M. 2010; 256 (2): 607-616

  Abstract

  To develop a method that combines parallel imaging and compressed sensing to enable faster and/or higher spatial resolution magnetic resonance (MR) imaging and show its feasibility in a pediatric clinical setting.Institutional review board approval was obtained for this HIPAA-compliant study, and informed consent or assent was given by subjects. A pseudorandom k-space undersampling pattern was incorporated into a three-dimensional (3D) gradient-echo sequence; aliasing then has an incoherent noiselike pattern rather than the usual coherent fold-over wrapping pattern. This k-space-sampling pattern was combined with a compressed sensing nonlinear reconstruction method that exploits the assumption of sparsity of medical images to permit reconstruction from undersampled k-space data and remove the noiselike aliasing. Thirty-four patients (15 female and 19 male patients; mean age, 8.1 years; range, 0-17 years) referred for cardiovascular, abdominal, and knee MR imaging were scanned with this 3D gradient-echo sequence at high acceleration factors. Obtained k-space data were reconstructed with both a traditional parallel imaging algorithm and the nonlinear method. Both sets of images were rated for image quality, radiologist preference, and delineation of specific structures by two radiologists. Wilcoxon and symmetry tests were performed to test the hypothesis that there was no significant difference in ratings for image quality, preference, and delineation of specific structures.Compressed sensing images were preferred more often, had significantly higher image quality ratings, and greater delineation of anatomic structures (P < .001) than did images obtained with the traditional parallel reconstruction method.A combination of parallel imaging and compressed sensing is feasible in a clinical setting and may provide higher resolution and/or faster imaging, addressing the challenge of delineating anatomic structures in pediatric MR imaging.

  View details for DOI 10.1148/radiol.10091218

  View details for Web of Science ID 000280272100032

  View details for PubMedID 20529991

  View details for PubMedCentralID PMC2909438

• SPIRiT: Iterative Self-consistent Parallel Imaging Reconstruction From Arbitrary k-Space MAGNETIC RESONANCE IN MEDICINE Lustig, M., Pauly, J. M. 2010; 64 (2): 457-471

  Abstract

  A new approach to autocalibrating, coil-by-coil parallel imaging reconstruction, is presented. It is a generalized reconstruction framework based on self-consistency. The reconstruction problem is formulated as an optimization that yields the most consistent solution with the calibration and acquisition data. The approach is general and can accurately reconstruct images from arbitrary k-space sampling patterns. The formulation can flexibly incorporate additional image priors such as off-resonance correction and regularization terms that appear in compressed sensing. Several iterative strategies to solve the posed reconstruction problem in both image and k-space domain are presented. These are based on a projection over convex sets and conjugate gradient algorithms. Phantom and in vivo studies demonstrate efficient reconstructions from undersampled Cartesian and spiral trajectories. Reconstructions that include off-resonance correction and nonlinear l(1)-wavelet regularization are also demonstrated.

  View details for DOI 10.1002/mrm.22428

  View details for Web of Science ID 000280422000017

  View details for PubMedID 20665790

• A Technique for Rapid Single-Echo Spin-Echo T-2 Mapping MAGNETIC RESONANCE IN MEDICINE Sussman, M. S., Vidarsson, L., Pauly, J. M., Cheng, H. M. 2010; 64 (2): 536-545

  Abstract

  A rapid technique for mapping of T(2) relaxation times is presented. The method is based on the conventional single-echo spin echo approach but uses a much shorter pulse repetition time to accelerate data acquisition. The premise of the new method is the use of a constant difference between the echo time and pulse repetition time, which removes the conventional and restrictive requirement of pulse repetition time > T(1). Theoretical and simulation investigations were performed to evaluate the criteria for accurate T(2) measurements. Measured T(2)s were shown to be within 1% error as long as the key criterion of pulse repetition time/T(2) > or =3 is met. Strictly, a second condition of echo time/T(1) < 1 is also required. However, violations of this condition were found to have minimal impact in most clinical scenarios. Validation was conducted in phantoms and in vivo T(2) mapping of healthy cartilage and brain. The proposed method offers all the advantages of single-echo spin echo imaging (e.g., immunity to stimulated echo effects, robustness to static field inhomogeneity, flexibility in the number and choice of echo times) in a considerably reduced amount of time and is readily implemented on any clinical scanner.

  View details for DOI 10.1002/mrm.22454

  View details for Web of Science ID 000280422000024

  View details for PubMedID 20665797

• Quantitative Tissue Characterization of Infarct Core and Border Zone in Patients With Ischemic Cardiomyopathy by Magnetic Resonance Is Associated With Future Cardiovascular Events JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Heidary, S., Patel, H., Chung, J., Yokota, H., Gupta, S. N., Bennett, M. V., Katikireddy, C., Nguyen, P., Pauly, J. M., Terashima, M., McConnell, M. V., Yang, P. C. 2010; 55 (24): 2762-2768

  Abstract

  This study evaluates how characterization of tissue heterogeneity of myocardial infarction by cardiovascular magnetic resonance (CMR) is associated with cardiovascular events (CVE) in patients with ischemic cardiomyopathy (ICM).Prior studies demonstrated that the quantification of myocardial scar volume by CMR is superior to left ventricular end-diastolic volume, left ventricular end-systolic volume, and left ventricular ejection fraction (LVEF) in predicting future CVE in ICM patients. Evaluation of infarct heterogeneity by measuring infarct core and border zones through CMR might have a higher association with CVE.Seventy patients (mean LVEF: 25 +/- 11%) considered for revascularization or medical management +/- implantable cardiac defibrillator were enrolled. A 1.5-T GE MRI (Signa, GE Healthcare, Milwaukee, Wisconsin) was used to acquire cine and delayed enhancement images. The patients' core and border zones of infarcted myocardium were analyzed and followed for CVE.Larger infarct border zone and its percentage of myocardium were found in the 29 patients (41%) who had CVE (median 13.3 g [interquartile range (IQR) 8.4 to 25.1 g] vs. 8.0 g [IQR 3.0 to 14.5 g], p = 0.02 and 7.8% [IQR 4.9% to 17.0%] vs. 4.1% [IQR 1.9% to 9.3%], p = 0.02, respectively). The core infarct zone and its percentage of myocardium, left ventricular end-diastolic volume, left ventricular end-systolic volume, and LVEF were not statistically significant. Sub-analysis of the medical management and revascularization patients with CVE demonstrated that the medically managed patients had a larger border zone, whereas there was no difference between border and core zones in the revascularization group (p < 0.05).Quantification of core and border zones and their percentages of myocardium through CMR is associated with future CVE and might assist in the management of patients with ICM.

  View details for DOI 10.1016/j.jacc.2010.01.052

  View details for PubMedID 20538171

• Frequency-Offset Cartesian Feedback Based on Polyphase Difference Amplifiers IEEE TRANSACTIONS ON MICROWAVE THEORY AND TECHNIQUES Zanchi, M. G., Pauly, J. M., Scott, G. C. 2010; 58 (5): 1297-1308

  Abstract

  A modified Cartesian feedback method called "frequency-offset Cartesian feedback" and based on polyphase difference amplifiers is described that significantly reduces the problems associated with quadrature errors and DC-offsets in classic Cartesian feedback power amplifier control systems.In this method, the reference input and feedback signals are down-converted and compared at a low intermediate frequency (IF) instead of at DC. The polyphase difference amplifiers create a complex control bandwidth centered at this low IF, which is typically offset from DC by 200-1500 kHz. Consequently, the loop gain peak does not overlap DC where voltage offsets, drift, and local oscillator leakage create errors. Moreover, quadrature mismatch errors are significantly attenuated in the control bandwidth. Since the polyphase amplifiers selectively amplify the complex signals characterized by a +90° phase relationship representing positive frequency signals, the control system operates somewhat like single sideband (SSB) modulation. However, the approach still allows the same modulation bandwidth control as classic Cartesian feedback.In this paper, the behavior of the polyphase difference amplifier is described through both the results of simulations, based on a theoretical analysis of their architecture, and experiments. We then describe our first printed circuit board prototype of a frequency-offset Cartesian feedback transmitter and its performance in open and closed loop configuration. This approach should be especially useful in magnetic resonance imaging transmit array systems.

  View details for DOI 10.1109/TMTT.2010.2045579

  View details for Web of Science ID 000277660200026

  View details for PubMedCentralID PMC2929980

• Frequency-Offset Cartesian Feedback Based on Polyphase Difference Amplifiers. IEEE transactions on microwave theory and techniques Zanchi, M. G., Pauly, J. M., Scott, G. C. 2010; 58 (5): 1297-1308

  Abstract

  A modified Cartesian feedback method called "frequency-offset Cartesian feedback" and based on polyphase difference amplifiers is described that significantly reduces the problems associated with quadrature errors and DC-offsets in classic Cartesian feedback power amplifier control systems.In this method, the reference input and feedback signals are down-converted and compared at a low intermediate frequency (IF) instead of at DC. The polyphase difference amplifiers create a complex control bandwidth centered at this low IF, which is typically offset from DC by 200-1500 kHz. Consequently, the loop gain peak does not overlap DC where voltage offsets, drift, and local oscillator leakage create errors. Moreover, quadrature mismatch errors are significantly attenuated in the control bandwidth. Since the polyphase amplifiers selectively amplify the complex signals characterized by a +90° phase relationship representing positive frequency signals, the control system operates somewhat like single sideband (SSB) modulation. However, the approach still allows the same modulation bandwidth control as classic Cartesian feedback.In this paper, the behavior of the polyphase difference amplifier is described through both the results of simulations, based on a theoretical analysis of their architecture, and experiments. We then describe our first printed circuit board prototype of a frequency-offset Cartesian feedback transmitter and its performance in open and closed loop configuration. This approach should be especially useful in magnetic resonance imaging transmit array systems.

  View details for DOI 10.1109/TMTT.2010.2045579

  View details for PubMedID 20814450

  View details for PubMedCentralID PMC2929980

• Variable-Density Parallel Imaging With Partially Localized Coil Sensitivities IEEE TRANSACTIONS ON MEDICAL IMAGING Cukur, T., Santos, J. M., Pauly, J. M., Nishimura, D. G. 2010; 29 (5): 1173-1181

  Abstract

  Partially parallel imaging with localized sensitivities is a fast parallel image reconstruction method for both Cartesian and non-Cartesian trajectories, but suffers from aliasing artifacts when there are deviations from the assumption of perfect localization. Such reconstructions would normally crop the individual coil images to remove the artifacts prior to combination. However, the sampling densities in variable-density k-space trajectories support different field-of-views for separate regions in k -space. In fact, the higher sampling density of low frequencies can be used to reconstruct a bigger field-of-view without introducing aliasing artifacts and the resulting image signal-to-noise ratio (SNR) can be improved. A novel, fast variable-density parallel imaging method is presented, which reconstructs different field-of-views from separate frequencies according to the local sampling density in k-space. Aliasing-suppressed images can be produced with high SNR-efficiency without the need for accurate estimation of coil sensitivities and complex or iterative computations.

  View details for DOI 10.1109/TMI.2010.2042805

  View details for Web of Science ID 000277336700006

  View details for PubMedID 20236876

  View details for PubMedCentralID PMC3155390

• Accelerated Slice Encoding for Metal Artifact Correction JOURNAL OF MAGNETIC RESONANCE IMAGING Hargreaves, B. A., Chen, W., Lu, W., Alley, M. T., Gold, G. E., Brau, A. C., Pauly, J. M., Pauly, K. B. 2010; 31 (4): 987-996

  Abstract

  To demonstrate accelerated imaging with both artifact reduction and different contrast mechanisms near metallic implants.Slice-encoding for metal artifact correction (SEMAC) is a modified spin echo sequence that uses view-angle tilting and slice-direction phase encoding to correct both in-plane and through-plane artifacts. Standard spin echo trains and short-TI inversion recovery (STIR) allow efficient PD-weighted imaging with optional fat suppression. A completely linear reconstruction allows incorporation of parallel imaging and partial Fourier imaging. The signal-to-noise ratio (SNR) effects of all reconstructions were quantified in one subject. Ten subjects with different metallic implants were scanned using SEMAC protocols, all with scan times below 11 minutes, as well as with standard spin echo methods.The SNR using standard acceleration techniques is unaffected by the linear SEMAC reconstruction. In all cases with implants, accelerated SEMAC significantly reduced artifacts compared with standard imaging techniques, with no additional artifacts from acceleration techniques. The use of different contrast mechanisms allowed differentiation of fluid from other structures in several subjects.SEMAC imaging can be combined with standard echo-train imaging, parallel imaging, partial-Fourier imaging, and inversion recovery techniques to offer flexible image contrast with a dramatic reduction of metal-induced artifacts in scan times under 11 minutes.

  View details for DOI 10.1002/jmri.22112

  View details for Web of Science ID 000276328200026

  View details for PubMedID 20373445

  View details for PubMedCentralID PMC2894155

• Investigation of Tumor Hyperpolarized [1-C-13]-Pyruvate Dynamics Using Time-Resolved Multiband RF Excitation Echo-Planar MRSI MAGNETIC RESONANCE IN MEDICINE Larson, P. E., Bok, R., Kerr, A. B., Lustig, M., Hu, S., Chen, A. P., Nelson, S. J., Pauly, J. M., Kurhanewicz, J., Vigneron, D. B. 2010; 63 (3): 582-591

  Abstract

  Hyperpolarized [1-(13)C]-pyruvate is an exciting new agent for the in vivo study of cellular metabolism and a potential cancer biomarker. The nature of the hyperpolarized signal poses unique challenges because of its short duration and the loss of magnetization with every excitation. In this study, we applied a novel and efficient time-resolved MR spectroscopic imaging (MRSI) method to investigate in a prostate cancer model the localized temporal dynamics of the uptake of [1-(13)C]-pyruvate and its conversion to metabolic products, specifically [1-(13)C]-lactate. This hyperpolarized (13)C method used multiband excitation pulses for efficient use of the magnetization. This study demonstrated that regions of tumor were differentially characterized from normal tissue by the lactate dynamics, where tumors showed later lactate detection and longer lactate duration that was statistically significant (P < 0.001). Compared to late-pathologic-stage tumors, early- to intermediate-stage tumors demonstrated significantly (P < 0.01) lower lactate total signal-to-noise ratio (SNR), with similar temporal dynamic parameters. Hyperpolarized pyruvate dynamics provided uptake, perfusion, and vascularization information on tumors and normal tissue. Large, heterogeneous tumors demonstrated spatially variable uptake of pyruvate and metabolic conversion that was consistent with cellularity and necrosis identified by histology. The results of this study demonstrated the potential of this new hyperpolarized MR dynamic method for improved cancer detection and characterization.

  View details for DOI 10.1002/mrm.22264

  View details for Web of Science ID 000274938000006

  View details for PubMedID 20187172

  View details for PubMedCentralID PMC2844437

• 3D Compressed Sensing for Highly Accelerated Hyperpolarized C-13 MRSI With In Vivo Applications to Transgenic Mouse Models of Cancer MAGNETIC RESONANCE IN MEDICINE Hu, S., Lustig, M., Balakrishnan, A., Larson, P. E., Bok, R., Kurhanewicz, J., Nelson, S. J., Goga, A., Pauly, J. M., Vigneron, D. B. 2010; 63 (2): 312-321

  Abstract

  High polarization of nuclear spins in liquid state through hyperpolarized technology utilizing dynamic nuclear polarization has enabled the direct monitoring of (13)C metabolites in vivo at a high signal-to-noise ratio. Acquisition time limitations due to T(1) decay of the hyperpolarized signal require accelerated imaging methods, such as compressed sensing, for optimal speed and spatial coverage. In this paper, the design and testing of a new echo-planar (13)C three-dimensional magnetic resonance spectroscopic imaging (MRSI) compressed sensing sequence is presented. The sequence provides up to a factor of 7.53 in acceleration with minimal reconstruction artifacts. The key to the design is employing x and y gradient blips during a fly-back readout to pseudorandomly undersample k(f)-k(x)-k(y) space. The design was validated in simulations and phantom experiments where the limits of undersampling and the effects of noise on the compressed sensing nonlinear reconstruction were tested. Finally, this new pulse sequence was applied in vivo in preclinical studies involving transgenic prostate cancer and transgenic liver cancer murine models to obtain much higher spatial and temporal resolution than possible with conventional echo-planar spectroscopic imaging methods.

  View details for DOI 10.1002/mrm.22233

  View details for Web of Science ID 000273995200007

  View details for PubMedID 20017160

  View details for PubMedCentralID PMC2829256

• An Optically Coupled System for Quantitative Monitoring of MRI-Induced RF Currents Into Long Conductors IEEE TRANSACTIONS ON MEDICAL IMAGING Zanchi, M. G., Venook, R., Pauly, J. M., Scott, G. C. 2010; 29 (1): 169-178

  Abstract

  The currents induced in long conductors such as guidewires by the radio-frequency (RF) field in magnetic resonance imaging (MRI) are responsible for potentially dangerous heating of surrounding media, such as tissue. This paper presents an optically coupled system with the potential to quantitatively measure the RF currents induced on these conductors. The system uses a self shielded toroid transducer and active circuitry to modulate a high speed light-emitting-diode transmitter. Plastic fiber guides the light to a photodiode receiver and transimpedance amplifier. System validation included a series of experiments with bare wires that compared wire tip heating by fluoroptic thermometers with the RF current sensor response. Validations were performed on a custom whole body 64 MHz birdcage test platform and on a 1.5 T MRI scanner. With this system, a variety of phenomena were demonstrated including cable trap current attenuation, lossy dielectric Q-spoiling and even transverse electromagnetic wave node patterns. This system should find applications in studies of MRI RF safety for interventional devices such as pacemaker leads, and guidewires. In particular, variations of this device could potentially act as a realtime safety monitor during MRI guided interventions.

  View details for DOI 10.1109/TMI.2009.2031558

  View details for Web of Science ID 000273334400015

  View details for PubMedID 19758855

  View details for PubMedCentralID PMC2929568

• A Practical Acceleration Algorithm for Real-Time Imaging IEEE TRANSACTIONS ON MEDICAL IMAGING Suembuel, U., Santos, J. M., Pauly, J. M. 2009; 28 (12): 2042-2051

  Abstract

  A practical acceleration algorithm for real-time magnetic resonance imaging (MRI) is presented. Neither separate training scans nor embedded training samples are used. The Kalman filter based algorithm provides a fast and causal reconstruction of dynamic MRI acquisitions with arbitrary readout trajectories. The algorithm is tested against abrupt changes in the imaging conditions and offline reconstructions of in vivo cardiac MRI experiments are presented.

  View details for DOI 10.1109/TMI.2009.2030474

  View details for Web of Science ID 000272242100018

  View details for PubMedID 19709964

  View details for PubMedCentralID PMC3155727

• Combining Complex Signal Change in Functional MRI MAGNETIC RESONANCE IN MEDICINE Lee, J., Shahram, M., Pauly, J. M. 2009; 62 (5): 1358-1360

  View details for DOI 10.1002/mrm.22104

  View details for Web of Science ID 000271431200034

• Maximum Linear-Phase Spectral-Spatial Radiofrequency Pulses for Fat-Suppressed Proton Resonance Frequency-Shift MR Thermometry MAGNETIC RESONANCE IN MEDICINE Grissom, W. A., Kerr, A. B., Holbrook, A. B., Pauly, J. M., Butts-Pauly, K. 2009; 62 (5): 1242-1250

  Abstract

  Conventional spectral-spatial pulses used for water-selective excitation in proton resonance frequency-shift MR thermometry require increased sequence length compared to shorter wideband pulses. This is because spectral-spatial pulses are longer than wideband pulses, and the echo time period starts midway through them. Therefore, for a fixed echo time, one must increase sequence length to accommodate conventional spectral-spatial pulses in proton resonance frequency-shift thermometry. We introduce improved water-selective spectral-spatial pulses for which the echo time period starts near the beginning of excitation. Instead of requiring increased sequence length, these pulses extend into the long echo time periods common to PRF sequences. The new pulses therefore alleviate the traditional tradeoff between sequence length and fat suppression. We experimentally demonstrate an 11% improvement in frame rate in a proton resonance frequency imaging sequence compared to conventional spectral-spatial excitation. We also introduce a novel spectral-spatial pulse design technique that is a hybrid of previous model- and filter-based techniques and that inherits advantages from both. We experimentally validate the pulses' performance in suppressing lipid signal and in reducing sequence length compared to conventional spectral-spatial pulses.

  View details for DOI 10.1002/mrm.22118

  View details for Web of Science ID 000271431200018

  View details for PubMedID 19780177

  View details for PubMedCentralID PMC2795148

• Improved Time Series Reconstruction for Dynamic Magnetic Resonance Imaging IEEE TRANSACTIONS ON MEDICAL IMAGING Suembuel, U., Santos, J. M., Pauly, J. M. 2009; 28 (7): 1093-1104

  Abstract

  Time series of in vivo magnetic resonance images exhibit high levels of temporal correlation. Higher temporal resolution reconstructions are obtained by acquiring data at a fraction of the Nyquist rate and resolving the resulting aliasing using the correlation information. The dynamic imaging experiment is modeled as a linear dynamical system. A Kalman filter based unaliasing reconstruction is described for accelerated dynamic magnetic resonance imaging (MRI). The algorithm handles arbitrary readout trajectories naturally. The reconstruction is causal and very fast, making it applicable to real-time imaging. In vivo results are presented for cardiac MRI of healthy volunteers.

  View details for DOI 10.1109/TMI.2008.2012030

  View details for Web of Science ID 000267698100012

  View details for PubMedID 19150785

  View details for PubMedCentralID PMC2766564

• SEMAC: Slice Encoding for Metal Artifact Correction in MRI 16th Annual Meeting of the International-Society-of-Magnetic-Resonance-in-Medicine Lu, W., Pauly, K. B., Gold, G. E., Pauly, J. M., Hargreaves, B. A. WILEY-BLACKWELL. 2009: 66–76

  Abstract

  Magnetic resonance imaging (MRI) near metallic implants remains an unmet need because of severe artifacts, which mainly stem from large metal-induced field inhomogeneities. This work addresses MRI near metallic implants with an innovative imaging technique called "Slice Encoding for Metal Artifact Correction" (SEMAC). The SEMAC technique corrects metal artifacts via robust encoding of each excited slice against metal-induced field inhomogeneities. The robust slice encoding is achieved by extending a view-angle-tilting (VAT) spin-echo sequence with additional z-phase encoding. Although the VAT compensation gradient suppresses most in-plane distortions, the z-phase encoding fully resolves distorted excitation profiles that cause through-plane distortions. By positioning all spins in a region-of-interest to their actual spatial locations, the through-plane distortions can be corrected by summing up the resolved spins in each voxel. The SEMAC technique does not require additional hardware and can be deployed to the large installed base of whole-body MRI systems. The efficacy of the SEMAC technique in eliminating metal-induced distortions with feasible scan times is validated in phantom and in vivo spine and knee studies.

  View details for DOI 10.1002/mrm.21967

  View details for Web of Science ID 000267404300008

  View details for PubMedID 19267347

  View details for PubMedCentralID PMC2837371

• Self-Refocused Spatial-Spectral Pulse for Positive Contrast Imaging of Cells Labeled with SPIO Nanoparticles MAGNETIC RESONANCE IN MEDICINE Balchandani, P., Yamada, M., Pauly, J., Yang, P., Spielman, D. 2009; 62 (1): 183-192

  Abstract

  MRI has been used extensively to noninvasively track the location of cells labeled with superparamagnetic iron-oxide nanoparticles (SPIOs) in vivo. Typically, SPIOs are employed as a negative contrast agent which makes it difficult to differentiate labeled cells from extraneous sources of inhomogeneity and actual voids in the image. As a result, several novel approaches have been put forth to obtain positive contrast from SPIOs. One technique proposed by Cunningham et al. utilizes spectrally selective pulses to excite and refocus spins in the vicinity of the SPIOs. Although the frequency selectivity of this technique provides effective positive contrast, the lack of slice selectivity results in interfering signal from sources of off-resonance outside the slice of interest. We have developed a self-refocused spatial-spectral (SR-SPSP) pulse to achieve slice-selective spin-echo imaging of off-resonant spins. Using a self-refocused pulse affords flexibility in echo-time selection since the spin echo may be placed at any time after the end of the pulse. The spatial selectivity achieved by the SR-SPSP RF pulse eliminates background signal from out-of-slice regions and reduces the on-resonant water suppression requirements. Phantom and in vivo data demonstrate that positive contrast and slice-selectivity are achieved using this novel RF pulse.

  View details for DOI 10.1002/mrm.21973

  View details for PubMedID 19449385

• Time-Optimal Design for Multidimensional and Parallel Transmit Variable-Rate Selective Excitation MAGNETIC RESONANCE IN MEDICINE Lee, D., Lustig, M., Grissom, W. A., Pauly, J. M. 2009; 61 (6): 1471-1479

  Abstract

  Variable-rate selective excitation (VERSE) is a radio frequency (RF) pulse reshaping technique. It is most commonly used to reduce the peak magnitude and specific absorption rate (SAR) of RF pulses by reshaping pulses and gradient waveforms to reduce RF magnitude while preserving excitation profiles. In this work, a general time-optimal VERSE algorithm for multidimensional and parallel transmit pulses is presented. Time optimality is achieved by translating peak RF limits to gradient upper bounds in excitation k-space. The limits are fed into a time-optimal gradient waveform design technique. Effective SAR reduction is achieved by reducing peak RF subject to a fixed pulse length. The presented method is different from other VERSE techniques in that it provides a noniterative time-optimal multidimensional solution, which drastically simplifies VERSE designs. Examples are given for 1D and 2D single channel and 2D parallel transmit pulses.

  View details for DOI 10.1002/mrm.21950

  View details for Web of Science ID 000266429900022

  View details for PubMedID 19365849

  View details for PubMedCentralID PMC2764012

• Improved Shim Method Based on the Minimization of the Maximum Off-Resonance Frequency for Balanced Steady-State Free Precession (bSSFP) MAGNETIC RESONANCE IN MEDICINE Lee, J., Lustig, M., Kim, D., Pauly, J. M. 2009; 61 (6): 1500-1506

  Abstract

  In this work, a shim method that minimizes the maximum off-resonance frequency (min-max shim) in balanced steady-state free precession (bSSFP) is tested for brain imaging at 3T with constant and linear shim terms. The method demonstrates improvement of spatial coverage and banding artifact reduction over standard least-squares shimming. In addition, a new method (modified min-max shim) is introduced. This method reduces boundary band regions where the artifact is inevitable due to the excessive off-resonance frequency distribution. In comparison to standard least-squares shimming, the min-max based shim method either eliminates or reduces the size of banding artifacts. The method can be used to increase the signal-to-noise ratio (SNR) in bSSFP imaging or to increase the functional contrast in bSSFP functional MRI (fMRI) by allowing a longer usable repetition time (TR).

  View details for DOI 10.1002/mrm.21800

  View details for Web of Science ID 000266429900026

  View details for PubMedID 19319895

  View details for PubMedCentralID PMC2729138

• Double Half RF Pulses for Reduced Sensitivity to Eddy Currents in UTE Imaging MAGNETIC RESONANCE IN MEDICINE Josan, S., Pauly, J. M., Daniel, B. L., Pauly, K. B. 2009; 61 (5): 1083-1089

  Abstract

  Ultrashort echo time imaging with half RF pulse excitation is challenging as eddy currents induced by the slice-select gradient distort the half pulse slice profile. This work presents two pulses with T(2)-dependent slice profiles that are less sensitive to eddy currents. The double half pulse improves the slice selectivity for long T(2) components, while the inverted double half pulse suppresses the unwanted long T(2) signal. Thus, both approaches prevent imperfect cancellation of out-of-slice signal from contaminating the desired slice. Experimental results demonstrate substantially improved slice selectivity and R(2)* quantitation accuracy with these pulses. These pulses are effective in making short T(2) imaging and quantitation less sensitive to eddy currents and provide an alternative to time-consuming gradient characterization.

  View details for DOI 10.1002/mrm.21879

  View details for PubMedID 19235919

• Improved Half RF Slice Selectivity in the Presence of Eddy Currents with Out-of-Slice Saturation MAGNETIC RESONANCE IN MEDICINE Josan, S., Kaye, E., Pauly, J. M., Daniel, B. L., Pauly, K. B. 2009; 61 (5): 1090-1095

  Abstract

  Ultrashort echo time imaging with half RF pulse excitation is sensitive to eddy currents induced by the slice-select gradient that distorts the half pulse slice profile. This work demonstrates improvements in the half pulse profile by using spatial saturation on both sides of the imaged slice to suppress the out-of-slice magnetization. This effectively improves the selectivity of the half pulse excitation profile. A quadratic phase RF pulse with high bandwidth and selectivity was used to achieve a wide saturation band with sharp edges. Experimental results demonstrate substantially improved slice selectivity and R(2)* quantitation accuracy obtained with the out-of-slice saturation. This approach is effective in making short T(2) imaging and quantitation with half pulses less sensitive to eddy currents.

  View details for DOI 10.1002/mrm.21914

  View details for PubMedID 19319972

• Design of Cosine Modulated Very Selective Suppression Pulses for MR Spectroscopic Imaging at 3T MAGNETIC RESONANCE IN MEDICINE Osorio, J. A., Xu, D., Cunningham, C. H., Chen, A., Kerr, A. B., Pauly, J. M., Vigneron, D. B., Nelson, S. J. 2009; 61 (3): 533-540

  Abstract

  The advantages of using a 3 Tesla (T) scanner for MR spectroscopic imaging (MRSI) of brain tissue include improved spectral resolution and increased sensitivity. Very selective saturation (VSS) pulses are important for maximizing selectivity for PRESS MRSI and minimizing chemical shift misregistration by saturating signals from outside the selected region. Although three-dimensional (3D) PRESS MRSI is able to provide excellent quality metabolic data for patients with brain tumors and has been shown to be important for defining tumor burden, the method is currently limited by how much of the anatomic lesion can be covered within a single examination. In this study we designed and implemented cosine modulated VSS pulses that were optimized for 3T MRSI acquisitions. This provided improved coverage and suppression of unwanted lipid signals with a smaller number of pulses. The use of the improved pulse sequence was validated in volunteer studies, and in clinical 3D MRSI exams of brain tumors.

  View details for DOI 10.1002/mrm.21842

  View details for Web of Science ID 000263608300005

  View details for PubMedID 19097232

  View details for PubMedCentralID PMC2690719

• REGULARIZED REFERENCELESS TEMPERATURE ESTIMATION IN PRF-SHIFT MR THERMOMETRY IEEE International Symposium on Biomedical Imaging - From Nano to Macro Grissom, W., Pauly, K. B., Lustig, M., Rieke, V., Pauly, J., McDannold, N. IEEE. 2009: 1235–1238

  View details for Web of Science ID 000270678400316

• Phased array 3D MR spectroscopic imaging of the brain at 7 T MAGNETIC RESONANCE IMAGING Xu, D., Cunningham, C. H., Chen, A. P., Li, Y., Kelley, D. A., Mukherjee, P., Pauly, J. M., Nelson, S. J., Vigneron, D. B. 2008; 26 (9): 1201-1206

  Abstract

  Ultra-high-field 7 T magnetic resonance (MR) scanners offer the potential for greatly improved MR spectroscopic imaging due to increased sensitivity and spectral resolution. Prior 7 T human single-voxel MR Spectroscopy (MRS) studies have shown significant increases in signal-to-noise ratio (SNR) and spectral resolution as compared to lower magnetic fields but have not demonstrated the increase in spatial resolution and multivoxel coverage possible with 7 T MR spectroscopic imaging. The goal of this study was to develop specialized radiofrequency (RF) pulses and sequences for three-dimensional (3D) MR spectroscopic imaging (MRSI) at 7 T to address the challenges of increased chemical shift misregistration, B1 power limitations, and increased spectral bandwidth. The new 7 T MRSI sequence was tested in volunteer studies and demonstrated the feasibility of obtaining high-SNR phased-array 3D MRSI from the human brain.

  View details for DOI 10.1016/j.mri.2008.03.006

  View details for Web of Science ID 000261085500001

  View details for PubMedID 18486386

  View details for PubMedCentralID PMC2821191

• Multiband excitation pulses for hyperpolarized C-13 dynamic chemical-shift imaging JOURNAL OF MAGNETIC RESONANCE Larson, P. E., Kerr, A. B., Chen, A. P., Lustig, M. S., Zierhut, M. L., Hu, S., Cunningham, C. H., Pauly, J. M., Kurhanewicz, J., Vigneron, D. B. 2008; 194 (1): 121-127

  Abstract

  Hyperpolarized 13C offers high signal-to-noise ratios for imaging metabolic activity in vivo, but care must be taken when designing pulse sequences because the magnetization cannot be recovered once it has decayed. It has a short lifetime, on the order of minutes, and gets used up by each RF excitation. In this paper, we present a new dynamic chemical-shift imaging method that uses specialized RF pulses designed to maintain most of the hyperpolarized substrate while providing adequate SNR for the metabolic products. These are multiband, variable flip angle, spectral-spatial RF pulses that use spectral selectivity to minimally excite the injected prepolarized 13C-pyruvate substrate. The metabolic products of lactate and alanine are excited with a larger flip angle to increase SNR. This excitation was followed by an RF amplitude insensitive double spin-echo and an echo-planar flyback spectral-spatial readout gradient. In vivo results in rats and mice are presented showing improvements over constant flip angle RF pulses. The metabolic products are observable for a longer window because the low pyruvate flip angle preserves magnetization, allowing for improved observation of spatially varying metabolic reactions.

  View details for DOI 10.1016/j.jmr.2008.06.010

  View details for Web of Science ID 000258938100017

  View details for PubMedID 18619875

• Pulse sequence for dynamic volumetric imaging of hyperpolarized metabolic products JOURNAL OF MAGNETIC RESONANCE Cunningham, C. H., Chen, A. P., Lustig, M., Hargreaves, B. A., Lupo, J., Xu, D., Kurhanewicz, J., Hurd, R. E., Pauly, J. M., Nelson, S. J., Vigneron, D. B. 2008; 193 (1): 139-146

  Abstract

  Dynamic nuclear polarization and dissolution of a (13)C-labeled substrate enables the dynamic imaging of cellular metabolism. Spectroscopic information is typically acquired, making the acquisition of dynamic volumetric data a challenge. To enable rapid volumetric imaging, a spectral-spatial excitation pulse was designed to excite a single line of the carbon spectrum. With only a single resonance present in the signal, an echo-planar readout trajectory could be used to resolve spatial information, giving full volume coverage of 32 x 32 x 16 voxels every 3.5s. This high frame rate was used to measure the different lactate dynamics in different tissues in a normal rat model and a mouse model of prostate cancer.

  View details for DOI 10.1016/j.jmr.2008.03.012

  View details for Web of Science ID 000256891700019

  View details for PubMedID 18424203

  View details for PubMedCentralID PMC3051833

• Improved slice selection for R2*mapping during cryoablation with eddy current compensation JOURNAL OF MAGNETIC RESONANCE IMAGING Lu, A., Daniel, B. L., Pauly, J. M., Pauly, K. B. 2008; 28 (1): 190-198

  Abstract

  To improve the slice profile and image quality of R2* mapping in the iceball during cryoablation with ultrashort echo time (UTE) imaging by compensating for eddy currents induced by the selective gradient when half-pulse radiofrequency (RF) excitation is employed to achieve UTEs.A method to measure both B0 and linear eddy currents simultaneously is first presented. This is done with a least-square fitting process on calibration data collected on a phantom. Eddy currents during excitation are compensated by redesigning the RF pulse and the selective gradient accordingly, while that resultant from the readout gradient are compensated for during image reconstruction. In vivo data were obtained continuously during the cryoablation experiments to calculate the R2* values in the iceball and to correlate them with the freezing process.Image quality degradation due to eddy currents is significantly reduced with the proposed approaches. R2* maps of iceball throughout the cryoablation experiments were achieved with improved quality.The proposed approaches are effective for compensating eddy currents during half-pulse RF excitation as well as readout. TEs as short as 100 microsec were obtained, allowing R2* maps to be obtained from frozen tissues with improved quality.

  View details for DOI 10.1002/jmri.21396

  View details for PubMedID 18581340

• A fast method for designing time-optimal gradient waveforms for arbitrary k-space trajectories IEEE TRANSACTIONS ON MEDICAL IMAGING Lustig, M., Kim, S., Pauly, J. A. 2008; 27 (6): 866-873

  Abstract

  A fast and simple algorithm for designing time-optimal waveforms is presented. The algorithm accepts a given arbitrary multidimensional k-space trajectory as the input and outputs the time-optimal gradient waveform that traverses k-space along that path in minimum time. The algorithm is noniterative, and its run time is independent of the complexity of the curve, i.e., the number of switches between slew-rate limited acceleration, slew-rate limited deceleration, and gradient amplitude limited regions. The key in the method is that the gradient amplitude is designed as a function of arc length along the k-space trajectory, rather than as a function of time. Several trajectory design examples are presented.

  View details for DOI 10.1109/TMI.2008.922699

  View details for Web of Science ID 000256354600013

  View details for PubMedID 18541493

  View details for PubMedCentralID PMC2928662

• Compressed sensing for resolution enhancement of hyperpolarized C-13 flyback 3D-MRSI JOURNAL OF MAGNETIC RESONANCE Hu, S., Lustig, M., Chen, A. P., Crane, J., Kerr, A., Kelley, D. A., Hurd, R., Kurhanewicz, J., Nelson, S. J., Pauly, J. M., Vigneron, D. B. 2008; 192 (2): 258-264

  Abstract

  High polarization of nuclear spins in liquid state through dynamic nuclear polarization has enabled the direct monitoring of 13C metabolites in vivo at very high signal-to-noise, allowing for rapid assessment of tissue metabolism. The abundant SNR afforded by this hyperpolarization technique makes high-resolution 13C 3D-MRSI feasible. However, the number of phase encodes that can be fit into the short acquisition time for hyperpolarized imaging limits spatial coverage and resolution. To take advantage of the high SNR available from hyperpolarization, we have applied compressed sensing to achieve a factor of 2 enhancement in spatial resolution without increasing acquisition time or decreasing coverage. In this paper, the design and testing of compressed sensing suited for a flyback 13C 3D-MRSI sequence are presented. The key to this design was the undersampling of spectral k-space using a novel blipped scheme, thus taking advantage of the considerable sparsity in typical hyperpolarized 13C spectra. Phantom tests validated the accuracy of the compressed sensing approach and initial mouse experiments demonstrated in vivo feasibility.

  View details for DOI 10.1016/j.jmr.2008.03.003

  View details for Web of Science ID 000256538300011

  View details for PubMedID 18367420

  View details for PubMedCentralID PMC2475338

• Interleaved narrow-band PRESS sequence with adiabatic spatial-spectral refocusing pulses for H-1 MRSI at 7T MAGNETIC RESONANCE IN MEDICINE Balchandani, P., Pauly, J., Spielman, D. 2008; 59 (5): 973-979

  Abstract

  Proton magnetic resonance spectroscopic imaging ((1)H MRSI) is a useful technique for measuring metabolite levels in vivo, with Choline (Cho), Creatine (Cre), and N-Acetyl-Aspartate (NAA) being the most prominent MRS-detectable brain biochemicals. (1)H MRSI at very high fields, such as 7T, offers the advantages of higher SNR and improved spectral resolution. However, major technical challenges associated with high-field systems, such as increased B(1) and B(0) inhomogeneity as well as chemical shift localization (CSL) error, degrade the performance of conventional (1)H MRSI sequences. To address these problems, we have developed a Position Resolved Spectroscopy (PRESS) sequence with adiabatic spatial-spectral (SPSP) refocusing pulses, to acquire multiple narrow spectral bands in an interleaved fashion. The adiabatic SPSP pulses provide magnetization profiles that are largely invariant over the 40% B(1) variation measured across the brain at 7T. Additionally, there is negligible CSL error since the transmit frequency is separately adjusted for each spectral band. in vivo (1)H MRSI data were obtained from the brain of a normal volunteer using a standard PRESS sequence and the interleaved narrow-band PRESS sequence with adiabatic refocusing pulses. In comparison with conventional PRESS, this new approach generated high-quality spectra from an appreciably larger region of interest and achieved higher overall SNR.

  View details for DOI 10.1002/mrm.21539

  View details for Web of Science ID 000255230700005

  View details for PubMedID 18429014

  View details for PubMedCentralID PMC2692522

• Slice-selective tunable-flip adiabatic low peak-power excitation pulse MAGNETIC RESONANCE IN MEDICINE Balchandani, P., Pauly, J., Spielman, D. 2008; 59 (5): 1072-1078

  Abstract

  Adiabatic pulses are useful in achieving uniform excitation profiles in the presence of B(1)-inhomogeneity. At higher fields, this inhomogeneity becomes more severe, further amplifying the need for B(1)-insensitive excitation. Although gradient modulation techniques for slice-selective adiabatic excitation have been introduced, a pulse that falls within the gradient and RF amplifier limits for most commercial human scanners is currently unavailable. In this work, we present an alternative gradient modulated approach for pulse design that achieves adiabatic slice selection with significantly lower RF peak power requirements. The resulting Slice-selective Tunable-flip AdiaBatic Low peak-power Excitation (STABLE) pulse consists of an oscillating gradient in conjunction with a BIR-4-like RF envelope that is sampled by many short spatial subpulses to achieve spatial selectivity. Simulations show that the expected spatial profile as well as the off-resonance behavior of the pulse remain invariant for a range of B(1) values. Phantom and in vivo results demonstrate the adiabaticity and slice selectivity of the STABLE pulse.

  View details for DOI 10.1002/mrm.21540

  View details for Web of Science ID 000255230700017

  View details for PubMedID 18429017

  View details for PubMedCentralID PMC2692433

• Full-brain coverage and high-resolution Imaging capabilities of passband b-SSFP fMRI at 3T MAGNETIC RESONANCE IN MEDICINE Lee, J. H., Dumoulin, S. O., Saritas, E. U., Glover, G. H., Wandell, B. A., Nishimura, D. G., Pauly, J. M. 2008; 59 (5): 1099-1110

  Abstract

  Passband balanced-steady-state free precession (b-SSFP) fMRI is a recently developed method that utilizes the passband (flat portion) of the b-SSFP off-resonance response to measure MR signal changes elicited by changes in tissue oxygenation following increases in neuronal activity. Rapid refocusing and short readout durations of b-SSFP, combined with the relatively large flat portion of the b-SSFP off-resonance spectrum allows distortion-free full-brain coverage with only two acquisitions. This allows for high-resolution functional imaging, without the spatial distortion frequently encountered in conventional high-resolution functional images. Finally, the 3D imaging compatibility of the b-SSFP acquisitions permits isotropic-voxel-size high-resolution acquisitions. In this study we address some of the major technical issues involved in obtaining passband b-SSFP-based functional brain images with practical imaging parameters and demonstrate the advantages through breath-holding and visual field mapping experiments.

  View details for DOI 10.1002/mrm.21576

  View details for Web of Science ID 000255230700020

  View details for PubMedID 18421687

  View details for PubMedCentralID PMC2694041

• Quantitative characterization of myocardial infarction by cardiovascular magnetic resonance predicts future cardiovascular events in patients with ischemic cardiomyopathy JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE Yokota, H., Heidary, S., Katikireddy, C. K., Nguyen, P., Pauly, J. M., McConnell, M. V., Yang, P. C. 2008; 10

  Abstract

  Cardiovascular magnetic resonance (CMR) can provide quantitative data of the myocardial tissue utilizing high spatial and temporal resolution along with exquisite tissue contrast. Previous studies have correlated myocardial scar tissue with the occurrence of ventricular arrhythmia. This study was conducted to evaluate whether characterization of myocardial infarction by CMR can predict cardiovascular events in patients with ischemic cardiomyopathy (ICM).We consecutively studied 86 patients with ICM (LVEF < 50%, mean LVEF: 26 +/- 12%) with CMR before revascularization or medication therapy +/- implantable cardiac defibrillator, determined the amount of myocardial scar, and followed for development of cardiovascular events. Thirty-three patients (38%) had cardiovascular events (mean follow-up: 20 +/- 16 months). Patients who developed cardiovascular events had larger scar volume and scar percentage of the myocardium than those who did not develop cardiovascular events (16.8 +/- 12.4 cm3 vs. 11.7 +/- 12.6 cm3, p = 0.023 and 10.2 +/- 6.9% vs. 7.2 +/- 6.7%, p = 0.037, respectively). There were no significant differences in LVEDV, LVESV and LVEF between the patients with and without cardiovascular events (231 +/- 76 ml vs. 230 +/- 88 ml; 180 +/- 73 ml vs. 175 +/- 90 ml; and 25 +/- 10% vs. 27 +/- 13%, respectively).Quantification of the scar volume and scar percentage by CMR is superior to LVEDV, LVESV, and LVEF in prognosticating the future likelihood of the development of cardiovascular events in patients with ICM.

  View details for DOI 10.1186/1532-429X-10-17

  View details for PubMedID 18400089

• Reduction of truncation artifacts in rapid 3D articular cartilage imaging JOURNAL OF MAGNETIC RESONANCE IMAGING Rakow-Penner, R., Gold, G., Daniel, B., Stevens, K., Rosenberg, J., Mazin, S. 2008; 27 (4): 860-865

  Abstract

  To reduce Gibbs ringing artifact in three-dimensional (3D) articular knee cartilage imaging with linear prediction (LP).A reconstruction method using LP in 3D was applied to truncated data sets of six healthy knees. The technique first linearizes the data before applying the prediction algorithm. Three radiologists blindly reviewed and ranked images of the full, truncated, and predicted data sets. Statistical analysis of the radiologists' reviews was performed for image quality, clinical acceptability of the images, and equivalence with the gold standard.LP applied to 3D knee cartilage imaging allows for 40% decreased scan time while providing image quality with statistical equivalence to a full data set.3D spoiled gradient echo imaging (SPGR) knee cartilage imaging requires significant scan time. This 40% reduction in scan time will allow such scans to be more feasible without sacrificing clinical acceptability.

  View details for DOI 10.1002/jmri.21312

  View details for PubMedID 18383247

• Compressed sensing MRI IEEE SIGNAL PROCESSING MAGAZINE Lustig, M., Donoho, D. L., Santos, J. M., Pauly, J. M. 2008; 25 (2): 72-82

  View details for Web of Science ID 000254471100011

• Varying kernel-extent gridding reconstruction for undersampled variable-density spirals MAGNETIC RESONANCE IN MEDICINE Cukur, T., Santos, J. M., Nishimura, D. G., Pauly, J. M. 2008; 59 (1): 196-201

  Abstract

  Nonuniform, non-Cartesian k-space trajectories enable fast scanning with reduced motion and flow artifacts. In such cases, the data are usually convolved with a kernel and resampled onto a Cartesian grid before reconstruction. For trajectories such as undersampled variable-density spirals, the mainlobe width of the kernel for undersampled high spatial frequencies has to be larger to limit the amount of aliasing energy. Continuously varying the kernel extent is time consuming. By dividing k-space into several annuli and using appropriate mainlobe widths for each, the aliasing energy and noise can be reduced at the expense of lower resolution towards the edge of the field of view (FOV). Resolution can instead be preserved at the center of the FOV, which is expected to be free of artifacts, without any artifact reduction. The image reconstructed from each annulus can be deapodized separately. The method can be applied to most k-space trajectories used in MRI.

  View details for DOI 10.1002/mrm.21329

  View details for Web of Science ID 000251979600025

  View details for PubMedID 18050316

• Noise performance of a precision pulsed electromagnet power supply for magnetic resonance imaging IEEE TRANSACTIONS ON MEDICAL IMAGING Matter, N. I., Chronik, B., Pauly, J. M., Macovski, A., Conolly, S. M., Scott, G. C. 2008; 27 (1): 75-86

  Abstract

  Prepolarized magnetic resonance imaging (PMRI) uses two pulsed electromagnets to achieve high-field image quality with the benefits of low-field data acquisition. The principal challenge with all resistive MRI systems is the implementation of a highly precise magnet current supply. The noise current through the magnet is fundamentally limited by the current transducer used to provide feedback and the voltage reference used to generate the demand signal. Field instability in the main field magnet can both corrupt the received data and degrade the robustness of Carr¿Purcell¿Meiboom¿Gill (CPMG) echo trains, which are paramount to efficient imaging in PMRI. In this work, we present the magnet control system that achieved sufficient field stability for PMRI at $0.5/0.13$ T, identify the dominant sources of noise in the control system, examine the imaging artifacts that can occur if the field stability is insufficient, and identify how the design can be improved for better field stability, should it be required for future implementations of PMRI.

  View details for DOI 10.1109/TMI.2007.903253

  View details for Web of Science ID 000252098300009

  View details for PubMedID 18270064

• Sparse MRI: The application of compressed sensing for rapid MR imaging MAGNETIC RESONANCE IN MEDICINE Lustig, M., Donoho, D., Pauly, J. M. 2007; 58 (6): 1182-1195

  Abstract

  The sparsity which is implicit in MR images is exploited to significantly undersample k-space. Some MR images such as angiograms are already sparse in the pixel representation; other, more complicated images have a sparse representation in some transform domain-for example, in terms of spatial finite-differences or their wavelet coefficients. According to the recently developed mathematical theory of compressed-sensing, images with a sparse representation can be recovered from randomly undersampled k-space data, provided an appropriate nonlinear recovery scheme is used. Intuitively, artifacts due to random undersampling add as noise-like interference. In the sparse transform domain the significant coefficients stand out above the interference. A nonlinear thresholding scheme can recover the sparse coefficients, effectively recovering the image itself. In this article, practical incoherent undersampling schemes are developed and analyzed by means of their aliasing interference. Incoherence is introduced by pseudo-random variable-density undersampling of phase-encodes. The reconstruction is performed by minimizing the l(1) norm of a transformed image, subject to data fidelity constraints. Examples demonstrate improved spatial resolution and accelerated acquisition for multislice fast spin-echo brain imaging and 3D contrast enhanced angiography.

  View details for DOI 10.1002/mrm.21391

  View details for Web of Science ID 000251346800013

  View details for PubMedID 17969013

• Hyperpolarized c-13 spectroscopic imaging of the TRAMP mouse at 3T - Initial experience MAGNETIC RESONANCE IN MEDICINE Chen, A. P., Albers, M. J., Cunningham, C. H., Kohler, S. J., Yen, Y., Hurd, R. E., Tropp, J., Bok, R., Pauly, J. M., Nelson, S. J., Kurhanewicz, J., Vigneron, D. B. 2007; 58 (6): 1099-1106

  Abstract

  The transgenic adenocarcinoma of mouse prostate (TRAMP) mouse is a well-studied murine model of prostate cancer with histopathology and disease progression that mimic the human disease. To investigate differences in cellular bioenergetics between normal prostate epithelial cells and prostate tumor cells, in vivo MR spectroscopic (MRS) studies with non-proton nuclei, such as (13)C, in the TRAMP model would be extremely useful. The recent development of a method for retaining dynamic nuclear polarization (DNP) in solution permits high signal-to-noise ratio (SNR) (13)C MRI or MRSI data to be obtained following injection of a hyperpolarized (13)C agent. In this transgenic mouse study, this method was applied using a double spin-echo (DSE) pulse sequence with a small-tip-angle excitation RF pulse, hyperbolic-secant refocusing pulses, and a flyback echo-planar readout trajectory for fast (10-14 s) MRSI of (13)C pyruvate (pyr) and its metabolic products at 0.135 cm(3) nominal spatial resolution. Elevated (13)C lactate (lac) was observed in both primary and metastatic tumors, demonstrating the feasibility of studying cellular bioenergetics in vivo with DNP hyperpolarized (13)C MRSI.

  View details for DOI 10.1002/mrm.21256

  View details for Web of Science ID 000251346800004

  View details for PubMedID 17969006

• Using adiabatic inversion pulses for long-T-2 suppression in ultrashort echo time (UTE) imaging MAGNETIC RESONANCE IN MEDICINE Larson, P. E., Conolly, S. M., Pauly, J. M., Nishimura, D. G. 2007; 58 (5): 952-961

  Abstract

  Ultrashort echo time (UTE) imaging is a technique that can visualize tissues with sub-millisecond T(2) values that have little or no signal in conventional MRI techniques. The short-T(2) tissues, which include tendons, menisci, calcifications, and cortical bone, are often obscured by long-T(2) tissues. This paper introduces a new method of long-T(2) component suppression based on adiabatic inversion pulses that significantly improves the contrast of short-T(2) tissues. Narrow bandwidth inversion pulses are used to selectively invert only long-T(2) components. These components are then suppressed by combining images prepared with and without inversion pulses. Fat suppression can be incorporated by combining images with the pulses applied on the fat and water resonances. Scaling factors must be used in the combination to compensate for relaxation during the preparation pulses. The suppression is insensitive to RF inhomogeneities because it uses adiabatic inversion pulses. Simulations and phantom experiments demonstrate the adiabatic pulse contrast and how the scaling factors are chosen. In vivo 2D UTE images in the ankle and lower leg show excellent, robust long-T(2) suppression for visualization of cortical bone and tendons.

  View details for DOI 10.1002/mrm.21341

  View details for Web of Science ID 000250560000013

  View details for PubMedID 17969119

  View details for PubMedCentralID PMC2942769

• Real-time MRI of peripheral chronic total occlusion interventions: Visualization of devices ex vivo in animals and lesions in vivo pre/post intervention in patients 19th Annual Transcatheter Cardiovascular Therapeutics Symposium Suzuki, Y., Overall, W. R., Santos, J. M., Terashima, M., Ikeno, F., Yeung, A. C., Pauly, J. M., McConnell, M. V., Williams, S. B. EXCERPTA MEDICA INC-ELSEVIER SCIENCE INC. 2007: 224L–224L

  View details for Web of Science ID 000250393900571

• Double spin-echo sequence for rapid spectroscopic imaging of hyperpolarized C-13 JOURNAL OF MAGNETIC RESONANCE Cunningham, C. H., Chen, A. P., Albers, M. J., Kurhanewicz, J., Hurd, R. E., Yen, Y., Pauly, J. M., Nelson, S. J., Vigneron, D. B. 2007; 187 (2): 357-362

  Abstract

  Dynamic nuclear polarization of metabolically active compounds labeled with (13)C has been introduced as a means for imaging metabolic processes in vivo. To differentiate between the injected compound and the various metabolic products, an imaging technique capable of separating the different chemical-shift species must be used. In this paper, the design and testing of a pulse sequence for rapid magnetic resonance spectroscopic imaging (MRSI) of hyperpolarized (13)C is presented. The pulse sequence consists of a small-tip excitation followed by a double spin echo using adiabatic refocusing pulses and a "flyback" echo-planar readout gradient. Key elements of the sequence are insensitivity to calibration of the transmit gain, the formation of a spin echo giving high-quality spectral information, and a small effective tip angle that preserves the magnetization for a sufficient duration. Experiments in vivo showed three-dimensional coverage with excellent spectral quality and SNR.

  View details for DOI 10.1016/j.jmr.2007.05.014

  View details for Web of Science ID 000248462800022

  View details for PubMedID 17562376

• T-2-selective magnetization preparation pulses IEEE TRANSACTIONS ON MEDICAL IMAGING Vidarsson, L., Cunningham, C., Gold, G. E., Pauly, J. A. 2007; 26 (7): 981-989

  Abstract

  The purpose of this work was to present and evaluate a new method for directly designing T2-selective preparation pulses. Using a modified Shinnar-Le-Roux (SLR) transform, the design of T2-selective pulses becomes equivalent to designing a pair of polynomials one of which represents the longitudinal magnetization and the other the transverse magnetization. The polynomials enable one to directly analyze the various tradeoffs involved in the design. To evaluate the new method, a short-T2-selective magnetization preparation pulse was designed. Following the preparation pulse, a 2D Fourier transform (2DFT) multislice gradient echo sequence was used for imaging. For verification Bloch equation simulations were performed along with both in vivo and phantom scans. Phantom scans showed good signal suppression of long-T2 species. This is supported by good long-T2 signal suppression seen on the in vivo images. Simulations indicate that the pulse is robust to +/-150 Hz B0 inhomogeneities and +/-10% B1 inhomogeneities.

  View details for DOI 10.1109/TMI.2007.897390

  View details for Web of Science ID 000247832700009

  View details for PubMedID 17649911

• High-speed 3T MR spectroscopic imaging of prostate with flyback echo-planar encoding JOURNAL OF MAGNETIC RESONANCE IMAGING Chen, A. P., Cunningham, C. H., Ozturk-Isik, E., Xu, D., Hurd, R. E., Kelley, D. A., Pauly, J. M., Kurhanewicz, J., Nelson, S. J., Vigneron, D. B. 2007; 25 (6): 1288-1292

  Abstract

  Prostate MR spectroscopic imaging (MRSI) at 3T may provide two-fold higher spatial resolution over 1.5T, but this can result in longer acquisition times to cover the entire gland using conventional phase-encoding. In this study, flyback echo-planar readout trajectories were incorporated into a Malcolm Levitt's composite-pulse decoupling sequence (MLEV)-point-resolved spectroscopy sequence (PRESS) to accelerate the acquisition of large array (16 x 16 x 8), high spatial (0.154 cm(3)) resolution MRSI data by eight-fold to just 8.5 minutes. Artifact free, high-quality MRSI data was obtained in nine prostate cancer patients. Easy data reconstruction and the robustness of the flyback echo-planar encoding make this technique particularly suitable for the clinical setting. The short acquisition time provided by this method reduces the 3T prostate MRI/MRSI exam time, allows longer repetition times, and/or allows the acquisition of additional MR acquisitions within the same exam.

  View details for DOI 10.1002/jmri.20916

  View details for Web of Science ID 000246824100025

  View details for PubMedID 17520729

• Complex data analysis in high-resolution SSFP fMRI MAGNETIC RESONANCE IN MEDICINE Lee, J., Shahram, M., Schwartzman, A., Pauly, J. M. 2007; 57 (5): 905-917

  Abstract

  In transition-band steady-state free precession (SSFP) functional MRI (fMRI), functional contrast originates from a bulk frequency shift induced by a deoxygenated hemoglobin concentration change in the activated brain regions. This frequency shift causes a magnitude and/or phase-signal change depending on the off-resonance distribution of a voxel in the balanced-SSFP (bSSFP) profile. However, in early low-resolution studies, only the magnitude signal activations were shown. In this paper the task-correlated phase-signal change is presented in a high-resolution (1 x 1 x 1 mm3) study. To include this phase activation in a functional analysis, a new complex domain data analysis method is proposed. The results show statistically significant phase-signal changes in a large number of voxels comparable to that of the magnitude-activated voxels. The complex-data analysis method successfully includes these phase activations in the activation map and thus provides wider coverage compared to magnitude-data analysis results.

  View details for DOI 10.1002/mrm.21195

  View details for Web of Science ID 000246052800013

  View details for PubMedID 17457883

• Independent phase modulation for efficient dual-band 3D imaging MAGNETIC RESONANCE IN MEDICINE Hargreaves, B. A., Cunningham, C. H., Pauly, J. M., Daniel, B. L. 2007; 57 (4): 798-802

  Abstract

  Certain applications of MRI, such as bilateral breast imaging, require simultaneous imaging of multiple volumes. Although image data can be acquired sequentially, the SNR is often improved if both slabs are excited and imaged together, typically with phase encoding across a volume including both slabs and the space between them. The use of independent phase modulation of multiple slabs eliminates the need to encode empty space between slabs, which can result in a significant time reduction. Each slab is excited with a phase proportional to phase-encode number such that the slab positions in the acquired data are shifted to reduce empty space. With careful consideration this technique is compatible with different pulse sequences (e.g., spin-echo, gradient-echo, RF spoiling, and balanced SSFP (bSSFP)) and acceleration strategies (e.g., partial k-space and parallel imaging). This technique was demonstrated in phantoms and applied to bilateral breast imaging, where scan times were reduced by 20-30%.

  View details for DOI 10.1002/mrm.21180

  View details for Web of Science ID 000245474600019

  View details for PubMedID 17390355

• Implementation of the Derivative Back Projection - Finite Hilbert Inverse algorithm in projection reconstruction MRI IEEE Nuclear Science Symposium/Medical Imaging Conference Barral, J. K., Pelc, N. J., Pauly, J. A., Nishimura, D. G. IEEE. 2007: 4083–4089

  View details for Web of Science ID 000257380403049

• Optimized Design of Single-sided Quadratic Phase Outer Volume Suppression Pulses for Magnetic Resonance Imaging 11th Mediterranean Conference on Medical and Biological Engineering and Computing (MEDICON 2007) Stikov, N., Mutapcic, A., Pauly, J. M. SPRINGER-VERLAG BERLIN. 2007: 423–25

  View details for Web of Science ID 000261088900108

• High-resolution 3D MR spectroscopic imaging of the prostate at 3 T with the MLEV-PRESS sequence MAGNETIC RESONANCE IMAGING Chen, A. P., Cunningham, C. H., Kurhanewicz, J., Xu, D., Hurd, R. E., Pauly, J. M., Carvajal, L., Karpodinis, K., Vigneron, D. B. 2006; 24 (7): 825-832

  Abstract

  A 3 T MLEV-point-resolved spectroscopy (PRESS) sequence employing optimized spectral-spatial and very selective outer-voxel suppression pulses was tested in 25 prostate cancer patients. At an echo time of 85 ms, the MLEV-PRESS sequence resulted in maximally upright inner resonances and minimal outer resonances of the citrate doublet of doublets. Magnetic resonance spectroscopic imaging (MRSI) exams performed at both 3 and 1.5 T for 10 patients demonstrated a 2.08+/-0.36-fold increase in signal-to-noise ratio (SNR) at 3 T as compared with 1.5 T for the center citrate resonances. This permitted the acquisition of MRSI data with a nominal spatial resolution of 0.16 cm3 at 3 T with similar SNR as the 0.34-cm3 data acquired at 1.5 T. Due to the twofold increase in spectral resolution at 3 T and the improved magnetic field homogeneity provided by susceptibility-matched endorectal coils, the choline resonance was better resolved from polyamine and creatine resonances as compared with 1.5 T spectra. In prostate cancer patients, the elevation of choline and the reduction of polyamines were more clearly observed at 3 T, as compared with 1.5 T MRSI. The increased SNR and corresponding spatial resolution obtainable at 3 T reduced partial volume effects and allowed improved detection of the presence and extent of abnormal metabolite levels in prostate cancer patients, as compared with 1.5 T MRSI.

  View details for DOI 10.1016/j.mri.2006.03.002

  View details for Web of Science ID 000240442800001

  View details for PubMedID 16916699

• Designing long-T-2 suppression pulses for ultrashort echo time imaging MAGNETIC RESONANCE IN MEDICINE Larson, P. E., Gurney, P. T., Nayak, K., Gold, G. E., Pauly, J. M., Nishimura, D. G. 2006; 56 (1): 94-103

  Abstract

  Ultrashort echo time (UTE) imaging has shown promise as a technique for imaging tissues with T2 values of a few milliseconds or less. These tissues, such as tendons, menisci, and cortical bone, are normally invisible in conventional magnetic resonance imaging techniques but have signal in UTE imaging. They are difficult to visualize because they are often obscured by tissues with longer T2 values. In this article, new long-T2 suppression RF pulses that improve the contrast of short-T2 species are introduced. These pulses are improvements over previous long-T2 suppression pulses that suffered from poor off-resonance characteristics or T1 sensitivity. Short-T2 tissue contrast can also be improved by suppressing fat in some applications. Dual-band long-T2 suppression pulses that additionally suppress fat are also introduced. Simulations, along with phantom and in vivo experiments using 2D and 3D UTE imaging, demonstrate the feasibility, improved contrast, and improved sensitivity of these new long-T2 suppression pulses. The resulting images show predominantly short-T2 species, while most long-T2 species are suppressed.

  View details for DOI 10.1002/mrm.20926

  View details for Web of Science ID 000238823600011

  View details for PubMedID 16724304

  View details for PubMedCentralID PMC2942755

• Saturated double-angle method for rapid B-1 plus mapping MAGNETIC RESONANCE IN MEDICINE Cunningham, C. H., Pauly, J. M., Nayak, K. S. 2006; 55 (6): 1326-1333

  Abstract

  For in vivo magnetic resonance imaging at high field (> or =3 T) it is essential to consider the homogeneity of the active B(1) field (B(1)+), particularly if surface coils are used for RF transmission. A new method is presented for highly rapid B(1)+ magnitude mapping. It combines the double angle method with a B(1)-insensitive magnetization-reset sequence such that the choice of repetition time (TR) is independent of T(1) and with a multislice segmented (spiral) acquisition to achieve volumetric coverage with adequate spatial resolution in a few seconds. Phantom experiments confirmed the accuracy of this technique even when TR < T(1), with the side effect being lowered SNR. The speed of this method enabled B(1)+ mapping in the chest and abdomen within a single breath-hold. In human cardiac imaging, the method enabled whole-heart coverage within a single 16-s breath-hold. Results from phantoms and healthy volunteers at 1.5 T and 3 T are presented.

  View details for DOI 10.1002/mrm.20896

  View details for Web of Science ID 000238051000013

  View details for PubMedID 16683260

• Linear combination filtering for T-2-selective imaging of the knee MAGNETIC RESONANCE IN MEDICINE Vidarsson, L., Gold, G. E., Hargreaves, B., Pauly, J. M. 2006; 55 (5): 1191-1196

  Abstract

  Recently a novel T2 selective imaging method based on linear combination (LC) filtering was developed. By linearly combining images acquired with different echo times LC filtering is able to generate images showing only tissues with a preselected range of T2 relaxation times. In this study the use of LC filtering in knee imaging was investigated. Three LC filters were designed: a short LC filter for imaging the knee meniscus, a medium LC filter for articular cartilage, and a long LC filter for synovial fluid. To verify the filter designs, eight phantoms with different T2 relaxation times were imaged. In addition, in vivo images were acquired from four asymptomatic volunteers and a subject with cartilage damage. T2 maps were also generated using the same source images. Signal-to-noise ratio (SNR) measurements were made of the meniscus, cartilage, and fluid regions on the three LC filtered images. The highest SNR was seen in the target tissue on each of the LC filtered images. LC filtering is a new method that can selectively image knee tissues based on their T2.

  View details for DOI 10.1002/mrm.20678

  View details for Web of Science ID 000237151600029

  View details for PubMedID 16586458

• Respiration-induced B-0 field fluctuation compensation in balanced SSFP: Real-time approach for transition-band SSFP fMRI MAGNETIC RESONANCE IN MEDICINE Lee, J., Santos, J. M., Conolly, S. M., Miller, K. L., Hargreaves, B. A., Pauly, J. M. 2006; 55 (5): 1197-1201

  Abstract

  In functional MRI (fMRI) the resonance frequency shift induced from respiration is a major source of physiological noise. In transition-band SSFP fMRI the respiration-induced resonance offset not only increases noise interference, it also shifts the activation band. This leads to a reduction in the contrast-to-noise ratio (CNR) and the potential for varying contrast levels during the experiment. A novel real-time method that compensates for the respiration-induced resonance offset frequency is presented. This method utilizes free induction decay (FID) phase information to measure the resonance offset. For compensation, one can update the resonant frequency in real time by changing the transmit RF pulse and receiver phases to track the measured offset. The results show decreased signal power in the respiration frequency band and increased numbers of activated voxels with higher Z-scores compared to uncompensated experiments.

  View details for DOI 10.1002/mrm.20879

  View details for Web of Science ID 000237151600030

  View details for PubMedID 16598728

• Examination of white matter in cocaine dependence 61st Annual Convention of the Society-of-Biological-Psychiatry Lim, K. O., Mueller, B. A., Specker, S. M., Pauly, J. M., Vidarsson, L., Wozniak, J. R. ELSEVIER SCIENCE INC. 2006: 111S–111S

  View details for Web of Science ID 000236767300358

• Single breath-hold whole-heart MRA using variable-density spirals at 3T MAGNETIC RESONANCE IN MEDICINE Santos, J. M., Cunningham, C. H., Lustig, M., Hargreaves, B. A., Hu, B. S., Nishimura, D. G., Pauly, J. M. 2006; 55 (2): 371-379

  Abstract

  Multislice breath-held coronary imaging techniques conventionally lack the coverage of free-breathing 3D acquisitions but use a considerably shorter acquisition window during the cardiac cycle. This produces images with significantly less motion artifact but a lower signal-to-noise ratio (SNR). By using the extra SNR available at 3 T and undersampling k-space without introducing significant aliasing artifacts, we were able to acquire high-resolution fat-suppressed images of the whole heart in 17 heartbeats (a single breath-hold). The basic pulse sequence consists of a spectral-spatial excitation followed by a variable-density spiral readout. This is combined with real-time localization and a real-time prospective shim correction. Images are reconstructed with the use of gridding, and advanced techniques are used to reduce aliasing artifacts.

  View details for DOI 10.1002/mrm.20765

  View details for Web of Science ID 000235326500019

  View details for PubMedID 16408262

• High-resolution FMRI at 1.5T using balanced SSFP MAGNETIC RESONANCE IN MEDICINE Miller, K. L., Smith, S. M., Jezzard, P., Pauly, J. M. 2006; 55 (1): 161-170

  Abstract

  The resolution in conventional BOLD FMRI is considerably lower than can be achieved with other MRI methods, and is insufficient for many important applications. One major difficulty in robustly improving spatial resolution is the poor image quality in BOLD FMRI, which suffers from distortions, blurring, and signal dropout. This work considers the potential for increased resolution with a new FMRI method based on balanced SSFP. This method establishes a blood oxygenation sensitive steady-state (BOSS) signal, in which the frequency sensitivity of balanced SSFP is used to detect the frequency shift of deoxyhemoglobin. BOSS FMRI is highly SNR efficient and does not suffer from image distortions or signal dropout, making this method an excellent candidate for high-resolution FMRI. This study presents the first demonstration of high-resolution BOSS FMRI, using an efficient 3D stack-of-segmented EPI readout and combined acquisition at multiple center frequencies. BOSS FMRI is shown to enable high-resolution FMRI data (1 x 1 x 2 mm(3)) in both visual and motor systems using standard hardware at 1.5 T. Currently, the major limitation of BOSS FMRI is its sensitivity to temporal and spatial field drift.

  View details for DOI 10.1002/mrm.20753

  View details for Web of Science ID 000234342800020

  View details for PubMedID 16345040

• Peri-infarct ischemia determined by cardiovascular magnetic resonance evaluation of myocardial viability and stress perfusion predicts future cardiovascular events in patients with severe ischemic cardiomyopathy JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE Tsukiji, M., Nguyen, P., Narayan, G., Hellinger, J., Chan, F., Herfkens, R., Pauly, J. M., McConnell, M. V., Yang, P. C. 2006; 8 (6): 773-779

  Abstract

  We assessed whether cardiovascular magnetic resonance imaging (CMR) of peri-infarct ischemia provides prognostic information in severe ischemic cardiomyopathy (ICM) patients referred for revascularization.Twenty-one patients with severe ICM were recruited prospectively for combined stress adenosine perfusion, late gadolinium enhancement, and rest perfusion studies. The patients were followed for in-hospital and post-discharge cardiovascular events.During 12+/- 9.8 months follow-up, 67% of the patients with peri-infarct ischemia and 13% of the patients without peri-infarct ischemia had cardiovascular events (p = 0.03). CONCLUSION. In severe ICM patients, the presence of peri-infarct ischemia was associated with a higher incidence of cardiovascular events.

  View details for DOI 10.1080/10976640600737615

  View details for PubMedID 17060098

• Real-time color-flow CMR in adults with congenital heart disease JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE de la Pena, E., Nguyen, P. K., Nayak, K. S., Yang, P. C., Rosenthal, D. N., Hu, B. S., Pauly, J. M., McConnell, M. V. 2006; 8 (6): 809-815

  Abstract

  CMR is valuable in the evaluation of congenital heart disease (CHD). Traditional flow imaging sequences involve cardiac and respiratory gating, increasing scan time and susceptibility to arrhythmias. We studied a real-time color-flow CMR system for the detection of flow abnormalities in 13 adults with CHD. All 16 congenital flow abnormalities previously detected by echocardiography were visualized using color-flow CMR, including atrial septal defects (n = 4), ventricular septal defects (n = 9), aortic coarctation (n = 1), Blalock-Taussig shunt (n = 1) and Fontan shunt (n = 1). Real-time color-flow CMR can identify intra- and extra-cardiac flow abnormalities in adults with congenital heart disease.

  View details for DOI 10.1080/10976640600777728

  View details for PubMedID 17060103

• Control over brain activation and pain learned by using real-time functional MRI PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA deCharms, R. C., Maeda, F., Glover, G. H., Ludlow, D., Pauly, J. M., Soneji, D., Gabrieli, J. D., Mackey, S. C. 2005; 102 (51): 18626-18631

  Abstract

  If an individual can learn to directly control activation of localized regions within the brain, this approach might provide control over the neurophysiological mechanisms that mediate behavior and cognition and could potentially provide a different route for treating disease. Control over the endogenous pain modulatory system is a particularly important target because it could enable a unique mechanism for clinical control over pain. Here, we found that by using real-time functional MRI (rtfMRI) to guide training, subjects were able to learn to control activation in the rostral anterior cingulate cortex (rACC), a region putatively involved in pain perception and regulation. When subjects deliberately induced increases or decreases in rACC fMRI activation, there was a corresponding change in the perception of pain caused by an applied noxious thermal stimulus. Control experiments demonstrated that this effect was not observed after similar training conducted without rtfMRI information, or using rtfMRI information derived from a different brain region, or sham rtfMRI information derived previously from a different subject. Chronic pain patients were also trained to control activation in rACC and reported decreases in the ongoing level of chronic pain after training. These findings show that individuals can gain voluntary control over activation in a specific brain region given appropriate training, that voluntary control over activation in rACC leads to control over pain perception, and that these effects were powerful enough to impact severe, chronic clinical pain.

  View details for DOI 10.1073/pnas.0505210102

  View details for Web of Science ID 000234174300068

  View details for PubMedID 16352728

  View details for PubMedCentralID PMC1311906

• High-resolution real-time spiral MRI for guiding vascular interventions in a rabbit model at 1.5 T. Journal of magnetic resonance imaging : JMRI Terashima, M., Hyon, M., de la Pena-Almaguer, E., Yang, P. C., Hu, B. S., Nayak, K. S., Pauly, J. M., McConnell, M. V. 2005; 22 (5): 687-690

  Abstract

  To study the feasibility of a combined high spatial and temporal resolution real-time spiral MRI sequence for guiding coronary-sized vascular interventions.Eight New Zealand White rabbits (four normal and four with a surgically-created stenosis in the abdominal aorta) were studied. A real-time interactive spiral MRI sequence combining 1.1 x 1.1 mm(2) in-plane resolution and 189-msec total image acquisition time was used to image all phases of an interventional procedure (i.e., guidewire placement, balloon angioplasty, and stenting) in the rabbit aorta using coronary-sized devices on a 1.5 T MRI system.Real-time spiral MRI identified all rabbit aortic stenoses and provided high-temporal-resolution visualization of guide-wires crossing the stenoses in all animals. Angioplasty balloon dilatation and deployment of coronary-sized copper stents in the rabbit aorta were also successfully imaged by real-time spiral MRI.Combining high spatial and temporal resolution with spiral MRI allows real-time MR-guided vascular intervention using coronary-sized devices in a rabbit model. This is a promising approach for guiding coronary interventions.

  View details for PubMedID 16217745

• High-resolution real-time spiral MRI for guiding vascular interventions in a rabbit model at 1L.5T JOURNAL OF MAGNETIC RESONANCE IMAGING Terashima, M., Hyon, M., De La Pena-Almaguer, E., Yang, P. C., Hu, B. S., Nayalk, K. S., Pauly, J. M., McConnell, M. V. 2005; 22 (5): 687-690

  Abstract

  To study the feasibility of a combined high spatial and temporal resolution real-time spiral MRI sequence for guiding coronary-sized vascular interventions.Eight New Zealand White rabbits (four normal and four with a surgically-created stenosis in the abdominal aorta) were studied. A real-time interactive spiral MRI sequence combining 1.1 x 1.1 mm(2) in-plane resolution and 189-msec total image acquisition time was used to image all phases of an interventional procedure (i.e., guidewire placement, balloon angioplasty, and stenting) in the rabbit aorta using coronary-sized devices on a 1.5 T MRI system.Real-time spiral MRI identified all rabbit aortic stenoses and provided high-temporal-resolution visualization of guide-wires crossing the stenoses in all animals. Angioplasty balloon dilatation and deployment of coronary-sized copper stents in the rabbit aorta were also successfully imaged by real-time spiral MRI.Combining high spatial and temporal resolution with spiral MRI allows real-time MR-guided vascular intervention using coronary-sized devices in a rabbit model. This is a promising approach for guiding coronary interventions.

  View details for DOI 10.1002/jmri.20409

  View details for Web of Science ID 000233096000015

• Design of flyback echo-planar readout gradients for magnetic resonance spectroscopic imaging MAGNETIC RESONANCE IN MEDICINE Cunningham, C. H., Vigneron, D. B., CHEN, A. P., Xu, D., Nelson, S. J., Hurd, R. E., Kelley, D. A., Pauly, J. M. 2005; 54 (5): 1286-1289

  Abstract

  The spatial resolution of conventional magnetic resonance spectroscopic imaging-(MRSI) is typically coarse, mainly due to SNR limitations. The increased signal available with higher field scanners and new array coils now permits higher spatial resolution, but conventional chemical shift imaging (phase encoding) limits the spatial coverage possible in a patient-acceptable acquisition time. The "flyback" echo-planar trajectory is particularly insensitive to errors and provides data that are simple to process. In this study, high-efficiency gradient waveforms for flyback echo-planar MRSI were designed and implemented. Normal volunteer studies at 3 T showed the feasibility of acquiring high spatial resolution with large coverage in a short scan time (2048 voxels in 2.3 min and 4096 voxels in 8.5 min). The trajectories were insensitive to errors in timing and require only a modest (10 to 30%) penalty in SNR relative to conventional phase encoding using the same acquisition time.

  View details for DOI 10.1002/mrm.20663

  View details for Web of Science ID 000233099700030

  View details for PubMedID 16187273

• Broadband multicoil imaging using multiple demodulation hardware: A feasibility study MAGNETIC RESONANCE IN MEDICINE Lee, J. H., Scott, G. C., Pauly, J. M., Nishimura, D. G. 2005; 54 (3): 669-676

  Abstract

  Multiple receiver-coil data collection is an effective approach to reduce scan time. There are many parallel imaging techniques that reduce scan time using multiple receiver coils. One of these methods, partially parallel imaging with localized sensitivities (PILS), utilizes the localized sensitivity of each coil. The advantages of PILS over other parallel imaging methods include the simplicity of the algorithm, good signal-to-noise ratio (SNR) properties, and the fact that there is no additional complexity involved in applying the algorithm to arbitrary k-space trajectories. This PILS method can be further improved to provide truly parallel broadband imaging with the use of multiple-demodulation hardware. By customizing the demodulation based on each coil's location, the k-space sampling rate can be chosen based on each coil's localized sensitivity region along the readout direction. A simulated demodulation of data from 2D Fourier transform (FT) and spiral trajectories is shown to demonstrate the method's feasibility.

  View details for DOI 10.1002/mrm.20595

  View details for Web of Science ID 000231494000018

  View details for PubMedID 16086362

• Variable-density one-shot Fourier velocity encoding MAGNETIC RESONANCE IN MEDICINE DiCarlo, J. C., Hargreaves, B. A., Nayak, K. S., Hu, B. S., Pauly, J. M., Nishimura, D. G. 2005; 54 (3): 645-655

  Abstract

  In areas of highly pulsatile and turbulent flow, real-time imaging with high temporal, spatial, and velocity resolution is essential. The use of 1D Fourier velocity encoding (FVE) was previously demonstrated for velocity measurement in real time, with fewer effects resulting from off-resonance. The application of variable-density sampling is proposed to improve velocity measurement without a significant increase in readout time or the addition of aliasing artifacts. Two sequence comparisons are presented to improve velocity resolution or increase the velocity field of view (FOV) to unambiguously measure velocities up to 5 m/s without aliasing. The results from a tube flow phantom, a stenosis phantom, and healthy volunteers are presented, along with a comparison of measurements using Doppler ultrasound (US). The studies confirm that variable-density acquisition of kz-kv space improves the velocity resolution and FOV of such data, with the greatest impact on the improvement of FOV to include velocities in stenotic ranges.

  View details for DOI 10.1002/mrm.20594

  View details for Web of Science ID 000231494000016

  View details for PubMedID 16088883

• Single-breathhold, four-dimensional, quantitative assessment of LV and RV function using triggered, real-time, steady-state free precession MRI in heart failure patients 12th Annual Meeting of the ISMRM Narayan, G., Nayak, K., Pauly, J., Hu, B. JOHN WILEY & SONS INC. 2005: 59–66

  Abstract

  To validate a novel, real-time, steady-state free precession (SSFP), single-breathhold technique for the assessment of left ventricular (LV) and right ventricular (RV) function in heart failure patients.A total of 20 heart failure patients (mean age 59 +/- 17 years) underwent scanning with our new, real-time, spiral SSFP sequence in which each cardiac phase was acquired in 118 msec at a resolution of 1.8 x 1.8 mm. Each cardiac slice (1-cm thick) was automatically advanced based on a cardiac trigger, allowing complete coverage of the heart in a single breathhold. The patients also underwent LV and RV assessment with the gold standard: multiple breathhold, cardiac-gated, segmented k-space strategy. LV and RV end-systolic volume (ESV) and end-diastolic volume (EDV) and LV mass were compared between the two imaging techniques.The new real-time strategy was highly concordant with the gold standard technique in the assessment of LVEDV (r = 0.98), LVESV (r = 0.98), RVESV (r = 0.86), RVEDV (r = 0.91), LVMASS (r = 0.95), RVEF (r = 0.70), and LVEF (r = 0.94). The mean bias (95% confidence interval [CI]) for each parameter is LVEDV: 10.6 cc (cm(3)) (3.8-17.4 cc), LVESV: -0.8 cc (-5.3 to 3.7 cc), RVEDV: 3.7 cc (-5.6 to 13.2 cc), RVESV: -3.1 cc (-11.1 to 4.9 cc), LVMASS: 26 g (12.4-39.8 g), RVEF: -2.9% (1.3 to -7.2 %), LVEF: 1.9% (5 to -1.1%). In addition, data acquisition was only nine +/- two seconds with the real-time strategy vs. 312 +/- 41 seconds for the standard technique.In patients with heart failure, real-time, spiral SSFP allows rapid and accurate assessment of RV and LV function in a single-breath hold. Using the same strategy, increased temporal resolution will allow real-time assessment of cardiac wall motion during stress studies.

  View details for DOI 10.1002/jmri.20358

  View details for Web of Science ID 000230128900008

  View details for PubMedID 15971180

• Spiral balanced steady-state free precession cardiac imaging MAGNETIC RESONANCE IN MEDICINE Nayak, K. S., Hargreaves, B. A., Hu, B. S., Nishimura, D. G., Pauly, J. M., Meyer, C. H. 2005; 53 (6): 1468-1473

  Abstract

  Balanced steady-state free precession (SSFP) sequences are useful in cardiac imaging because they achieve high signal efficiency and excellent blood-myocardium contrast. Spiral imaging enables the efficient acquisition of cardiac images with reduced flow and motion artifacts. Balanced SSFP has been combined with spiral imaging for real-time interactive cardiac MRI. New features of this method to enable scanning in a clinical setting include short, first-moment nulled spiral trajectories and interactive control over the spatial location of banding artifacts (SSFP-specific signal variations). The feasibility of spiral balanced SSFP cardiac imaging at 1.5 T is demonstrated. In observations from over 40 volunteer and patient studies, spiral balanced SSFP imaging shows significantly improved contrast compared to spiral gradient-spoiled imaging, producing better visualization of cardiac function, improved localization, and reduced flow artifacts from blood.

  View details for DOI 10.1002/mrm.20489

  View details for Web of Science ID 000229468200031

  View details for PubMedID 15906302

• X-ray compatible radiofrequency coil for magnetic resonance imaging MAGNETIC RESONANCE IN MEDICINE Rieke, V., GANGULY, A., Daniel, B. L., Scott, G., Pauly, J. M., Fahrig, R., Pelc, N. J., Butts, K. 2005; 53 (6): 1409-1414

  Abstract

  The range of RF coils that can be used in combined X-ray/MR (XMR) systems is limited because many conventional coils contain highly X-ray attenuating materials that are visible in the X-ray images and potentially obscure patient anatomy. In this study, an X-ray compatible coil design that has minimal X-ray attenuation in the field of view (FOV) of the X-ray image is presented. In this design, aluminum is used for the loop conductor and discrete elements of the coil are eliminated from the X-ray FOV. A surface coil and an abdominal phased array coil were built using the X-ray compatible design. X-ray attenuation and MR imaging properties of the coils were evaluated and compared to conventional coils. The X-ray compatible phased array coil was used to image patients during two interventional procedures in the XMR system. The X-ray compatible coils allowed for fluoroscopic X-ray image acquisition, without degradation by the coil, while maintaining excellent MR imaging qualities.

  View details for DOI 10.1002/mrm.20494

  View details for PubMedID 15906285

• Rapid gridding reconstruction with a minimal oversampling ratio IEEE TRANSACTIONS ON MEDICAL IMAGING Beatty, P. J., Nishimura, D. G., Pauly, J. M. 2005; 24 (6): 799-808

  Abstract

  Reconstruction of magnetic resonance images from data not falling on a Cartesian grid is a Fourier inversion problem typically solved using convolution interpolation, also known as gridding. Gridding is simple and robust and has parameters, the grid oversampling ratio and the kernel width, that can be used to trade accuracy for computational memory and time reductions. We have found that significant reductions in computation memory and time can be obtained while maintaining high accuracy by using a minimal oversampling ratio, from 1.125 to 1.375, instead of the typically employed grid oversampling ratio of two. When using a minimal oversampling ratio, appropriate design of the convolution kernel is important for maintaining high accuracy. We derive a simple equation for choosing the optimal Kaiser-Bessel convolution kernel for a given oversampling ratio and kernel width. As well, we evaluate the effect of presampling the kernel, a common technique used to reduce the computation time, and find that using linear interpolation between samples adds negligible error with far less samples than is necessary with nearest-neighbor interpolation. We also develop a new method for choosing the optimal presampled kernel. Using a minimal oversampling ratio and presampled kernel, we are able to perform a three-dimensional (3-D) reconstruction in one-eighth the time and requiring one-third the computer memory versus using an oversampling ratio of two and a Kaiser-Bessel convolution kernel, while maintaining the same level of accuracy.

  View details for DOI 10.1109/TMI.2005.848376

  View details for Web of Science ID 000229618700010

  View details for PubMedID 15959939

• Sequence design for magnetic resonance spectroscopic imaging of prostate cancer at 3T MAGNETIC RESONANCE IN MEDICINE Cunningham, C. H., Vigneron, D. B., Marjanska, M., CHEN, A. P., Xu, D., Hurd, R. E., Kurhanewicz, J., Garwood, M., Pauly, J. M. 2005; 53 (5): 1033-1039

  Abstract

  Magnetic resonance spectroscopic imaging (MRSI) has proven to be a powerful tool for the metabolic characterization of prostate cancer in patients before and following therapy. The metabolites that are of particular interest are citrate and choline because an increased choline-to-citrate ratio can be used as a marker for cancer. High-field systems offer the advantage of improved spectral resolution as well as increased magnetization. Initial attempts at extending MRSI methods to 3 T have been confounded by the J-modulation of the citrate resonances. A new pulse sequence is presented that controls the J-modulation of citrate at 3 T such that citrate is upright, with high amplitude, at a practical echo time. The design of short (14 ms) spectral-spatial refocusing pulses and trains of nonselective refocusing pulses are described. Phantom studies and simulations showed that upright citrate with negligible sidebands is observed at an echo time of 85 ms. Studies in a human subject verified that this behavior is reproduced in vivo and demonstrated that the water and lipid suppression of the new pulse sequence are sufficient for application in prostate cancer patients.

  View details for DOI 10.1002/mrm.20478

  View details for Web of Science ID 000228796900007

  View details for PubMedID 15844147

• POsitive contrast magnetic resonance imaging of cells labeled with magnetic nanoparticles MAGNETIC RESONANCE IN MEDICINE Cunningham, C. H., Arai, T., Yang, P. C., McConnell, M. V., Pauly, J. M., Conolly, S. M. 2005; 53 (5): 999-1005

  Abstract

  Contrast agents incorporating superparamagnetic iron-oxide nanoparticles have shown promise as a means to visualize labeled cells using MRI. Labeled cells cause significant signal dephasing due to the magnetic field inhomogeneity induced in water molecules near the cell. With the resulting signal void as the means for detection, the particles behave as a negative contrast agent, which can suffer from partial-volume effects. In this paper, a new method is described for imaging labeled cells with positive contrast. Spectrally selective RF pulses are used to excite and refocus the off-resonance water surrounding the labeled cells so that only the fluid and tissue immediately adjacent to the labeled cells are visible in the image. Phantom, in vitro, and in vivo experiments show the feasibility of the new method. A significant linear correlation (r = 0.87, P < 0.005) between the estimated number of cells and the signal was observed.

  View details for DOI 10.1002/mrm.20477

  View details for PubMedID 15844142

• Rapid musculoskeletal MRI with phase-sensitive steady-state free precession: Comparison with routine knee MRI AMERICAN JOURNAL OF ROENTGENOLOGY Vasanawala, S. S., Hargreaves, B. A., Pauly, J. M., Nishimura, D. G., Beaulieu, C. F., Gold, G. E. 2005; 184 (5): 1450-1455

  Abstract

  The aim of this work was to show the potential utility of a novel rapid 3D fat-suppressed MRI method for joint imaging.Phase-sensitive steady-state free precession provides rapid 3D joint imaging with robust fat suppression and excellent cartilage delineation.

  View details for Web of Science ID 000228875300013

  View details for PubMedID 15855095

• Echo time optimization for linear combination myelin Imaging MAGNETIC RESONANCE IN MEDICINE Vidarsson, L., Conolly, S. M., Lim, K. O., Gold, G. E., Pauly, J. M. 2005; 53 (2): 398-407

  Abstract

  A 3-echo linear combination myelin imaging method is presented. The echo times and weights are chosen such that the signal-to-noise ratio (SNR) of myelin-water is maximized, and signals from other white matter components are sufficiently suppressed. Interfering tissue water and cerebrospinal fluid (CSF) signals are much stronger than myelin due to their longer T2 and abundance. By carefully optimizing the echo times a 50-fold tissue water suppression is achieved along with a 10-fold CSF suppression. For comparison 4, 5, and 32 echo filters are also designed using the same method. The SNR efficiency of these filters is very similar. The 3-echo filter design was validated by phantom scans. In addition, multislice in vivo myelin images were acquired from both a healthy volunteer and a multiple sclerosis patient. Total scan time was 5 min. A uniform T2 filter is also designed to pass all white matter species with uniform gain. The myelin-water fraction of the in vivo 3-echo data set is then measured by dividing the myelin image by the uniformly filtered image. Obtained myelin-water fractions compare well with previous work.

  View details for DOI 10.1002/mrm.20360

  View details for Web of Science ID 000226651100018

  View details for PubMedID 15678534

• Reduction of blurring in view angle tilting MRI MAGNETIC RESONANCE IN MEDICINE Butts, K., Pauly, J. M., Gold, G. E. 2005; 53 (2): 418-424

  Abstract

  Magnetic resonance imaging (MRI) in the presence of metallic objects suffers from slice-selection errors and in-plane distortions. View angle tilting (VAT) corrects for in-plane distortions by adding a gradient on the slice-select axis during readout, but can suffer from image blurring. This work demonstrates that the major source of blurring is a slice profile modulation of the data, and proposes several solutions to prevent such blurring. Multiple high-bandwidth readouts are demonstrated to reduce the blurring while improving the signal-to-noise ratio (SNR) over a single high-bandwidth readout.

  View details for DOI 10.1002/mrm.20375

  View details for Web of Science ID 000226651100020

  View details for PubMedID 15678535

• Design of symmetric-sweep spectral-spatial RF pulses for spectral editing MAGNETIC RESONANCE IN MEDICINE Cunningham, C. H., Vigneron, D. B., CHEN, A. P., Xu, D., Hurd, R. E., Sailasuta, N., Pauly, J. M. 2004; 52 (1): 147-153

  Abstract

  Spectral-spatial RF (SSRF) pulses allow simultaneous selection in both frequency and spatial domains. These pulses are particularly important for clinical and research MR spectroscopy (MRS) applications for suppression of large water and lipid resonances. Also, the high bandwidth of the subpulses (5-10 kHz) greatly reduces the spatial-shift errors associated with different chemical shifts. However, the use of high-bandwidth subpulses along with enough spectral bandwidth to measure a typical range of metabolite frequencies (e.g., 300 Hz at 3 T) can require RF amplitudes beyond the limits of the RF amplifier of a typical scanner. In this article, a new method is described for designing nonlinear-phase 180 degrees SSRF pulses that can be used for spectral editing. The novel feature of the pulses is that the spectral profile develops as a symmetric sweep, from the outside edges of the spectral window towards the middle, so that coupled components are tipped simultaneously and over a short interval. Pulses were designed for lactate editing at 1.5 T and 3 T. The spectral and spatial spin-echo profiles of the new pulses were measured experimentally. Spectra acquired in phantom experiments showed a well-resolved, edited lactate doublet, with 91% to 93% editing efficiency.

  View details for DOI 10.1002/mrm.20116

  View details for Web of Science ID 000222491700020

  View details for PubMedID 15236378

• Referenceless PRF shift thermometry MAGNETIC RESONANCE IN MEDICINE Rieke, V., Vigen, K. K., Sommer, G., Daniel, B. L., Pauly, J. M., Butts, K. 2004; 51 (6): 1223-1231

  Abstract

  The proton resonance frequency (PRF) shift provides a means of measuring temperature changes during minimally invasive thermotherapy. However, conventional PRF thermometry relies on the subtraction of baseline images, which makes it sensitive to tissue motion and frequency drift during the course of treatment. In this study, a new method is presented that eliminates these problems by estimating the background phase from each acquired image phase. In this referenceless method, a polynomial is fit to the background phase outside the heated region in a weighted least-squares fit. Extrapolation of the polynomial to the heated region serves as the background phase estimate, which is then subtracted from the actual phase. The referenceless method is demonstrated on a phantom during laser heating, 0 degrees temperature rise images of in vivo human liver, interstitial laser ablation of porcine liver, and transurethral ultrasound ablation of canine prostate. A good correlation between temperature maps reconstructed with the referenceless and subtraction methods was found.

  View details for DOI 10.1002/mrm.20090

  View details for PubMedID 15170843

• Analysis of multiple-acquisition SSFP MAGNETIC RESONANCE IN MEDICINE Bangerter, N. K., Hargreaves, B. A., Vasanawala, S. S., Pauly, J. M., Gold, G. E., Nishimura, D. G. 2004; 51 (5): 1038-1047

  Abstract

  Refocused steady-state free precession (SSFP) is limited by its high sensitivity to local field variation, particularly at high field strengths or the long repetition times (TRs) necessary for high resolution. Several methods have been proposed to reduce SSFP banding artifact by combining multiple phase-cycled SSFP acquisitions, each differing in how individual signal magnitudes and phases are combined. These include maximum-intensity SSFP (MI-SSFP) and complex-sum SSFP (CS-SSFP). The reduction in SSFP banding is accompanied by a loss in signal-to-noise ratio (SNR) efficiency. In this work a general framework for analyzing banding artifact reduction, contrast, and SNR of any multiple-acquisition SSFP combination method is presented. A new sum-of-squares method is proposed, and a comparison is performed between each of the combination schemes. The sum-of-squares SSFP technique (SOS-SSFP) delivers both robust banding artifact reduction and higher SNR efficiency than other multiple-acquisition techniques, while preserving SSFP contrast.

  View details for DOI 10.1002/mrm.20052

  View details for Web of Science ID 000221239000022

  View details for PubMedID 15122688

• Real-time cardiac MRI at 3 tesla 11th Annual Meeting of the International-Society-for-Magnetic-Resonance-in-Medicine Nayak, K. S., Cunningham, C. H., Santos, J. M., Pauly, J. M. JOHN WILEY & SONS INC. 2004: 655–60

  Abstract

  Real-time cardiac and coronary MRI at 1.5T is relatively "signal starved" and the 3T platform is attractive for its immediate factor of two increase in magnetization. Cardiac imaging at 3T, however, is both subtly and significantly different from imaging at 1.5T because of increased susceptibility artifacts, differences in tissue relaxation, and RF homogeneity issues. New RF excitation and pulse sequence designs are presented which deal with the fat-suppression requirements and off-resonance issues at 3T. Real-time cardiac imaging at 3T is demonstrated with high blood SNR, blood-myocardium CNR, resolution, and image quality, using new spectral-spatial RF pulses and fast spiral gradient echo pulse sequences. The proposed sequence achieves 1.5 mm in-plane resolution over a 20 cm FOV, with a 5.52 mm measured slice thickness and 32 dB of lipid suppression. Complete images are acquired every 120 ms and are reconstructed and displayed at 24 frames/sec using a sliding window. Results from healthy volunteers show improved image quality, a 53% improvement in blood SNR efficiency, and a 232% improvement in blood-myocardium CNR efficiency compared to 1.5T.

  View details for DOI 10.1002/mrm.20053

  View details for Web of Science ID 000220557200002

  View details for PubMedID 15065236

• Steady-state diffusion-weighted imaging of in vivo knee cartilage MAGNETIC RESONANCE IN MEDICINE Miller, K. L., Hargreaves, B. A., Gold, G. E., Pauly, J. M. 2004; 51 (2): 394-398

  Abstract

  Diffusion-weighted imaging (DWI) has strong potential as a diagnostic for early cartilage damage, with clinical impact for diseases such as osteoarthritis. However, in vivo DWI of cartilage has proven difficult with conventional methods due to the short T2. This work presents a 3D steady-state DWI sequence that is able to image short-T2 species with high SNR. When combined with 2D navigator correction of motion-induced phase artifacts, this method enables high resolution in vivo DWI of cartilage. In vivo knee images in healthy subjects are presented with high SNR (SNR = 110) and submillimeter in-plane resolution (0.5 x 0.7 x 3.0 mm(3)). A method for fitting the diffusion coefficient is presented which produces fits within 10% of literature values. This method should be applicable to other short-T2 tissues, such as muscle, which are difficult to image using traditional DWI methods.

  View details for DOI 10.1002/mrm.10696

  View details for Web of Science ID 000188718600023

  View details for PubMedID 14755666

• Dynamic real-time architecture in magnetic resonance coronary angiography-a prospective clinical trial JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE Yang, P. C., Santos, J. M., Nguyen, P. K., Scott, G. C., Engvall, J., McConnell, M. V., Wright, G. A., Nishimura, D. G., Pauly, J. M., Hu, B. S. 2004; 6 (4): 885-894

  Abstract

  A dynamic real-time (dRT) architecture has been developed to address limitations in magnetic resonance coronary angiography (MRCA). A prospective clinical trial of 45 patients suspected of coronary artery disease was conducted to determine clinical utility of this integrated real-time system.Clinical implementation of MRCA is not performed routinely today. However, improved anatomic coverage, image quality, and scan flexibility may enhance its clinical utility. A novel real-time architecture addresses these challenges through instantaneous reconfiguration between real-time (RT) and high-resolution (HR) imaging sequences with dynamic selection of the desired element on a custom-designed receiver coil.A total of 45 subjects were recruited consecutively to evaluate scan time, anatomic coverage, image quality, and detection of coronary lesions. Using a modern PC, the dRT switches from RT to gated HR imaging sequence in one repetition time (39 ms). Magnetic resonance imaging (MRI) scanning was performed using a custom-designed coronary coil consisting of two four-inch phase-array circular elements enabled with real-time selection of the desired coil element.All studies were completed in less than 45 minutes and required a mean of 12 breath holds (16 heartbeats). Of the total number of coronary segments, 91% (357/394) were visualized. Excellent or good image quality was achieved in 86% of the segments. Blinded analysis of the coronary arteries revealed sensitivity of 93% and specificity of 88% in the detection of coronary stenoses.The integrated environment of dRT provides a rapid and flexible scan protocol for MRCA while achieving wide anatomical coverage, high image quality, and reliable detection of coronary stenosis in short scan time.

  View details for DOI 10.1016/j.JCMR.20036192

  View details for PubMedID 15646892

• Flexible real-time magnetic resonance imaging framework 26th Annual International Conference of the IEEE-Engineering-in-Medicine-and-Biology-Society Santos, G. M., Wright, G. A., Pauly, J. M. IEEE. 2004: 1048–1051

  View details for Web of Science ID 000225461800269

• Functional brain imaging with BOSSFMRI 26th Annual International Conference of the IEEE-Engineering-in-Medicine-and-Biology-Society Miller, K. L., Hargreaves, B. A., Lee, J. H., Ress, D., deCharms, R. C., Pauly, J. M. IEEE. 2004: 5234–5237

  View details for Web of Science ID 000225461801389

• Functional brain imaging with BOSS FMRI. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference Miller, K. L., Hargreaves, B. A., Lee, J., Ress, D., deCharms, R. C., Pauly, J. M. 2004; 7: 5234-5237

  Abstract

  The standard method for FMRI, using the blood oxygenation level dependent (BOLD) effect, has significant limitations that result from the coupling of functional contrast to sources of image artifact. We have developed an alternative method for FMRI based on balanced-SSFP imaging. This method uses the balanced-SSFP phase profile to invert the signal in deoxygenated blood relative to oxygenated blood. The resulting blood oxygenation sensitive steady-state (BOSS) signal decouples functional contrast from imaging, enabling significantly better image quality than BOLD FMRI. BOSS FMRI is very SNR-efficient, achieves strong functional contrast and is relatively immune to susceptibility gradients. In this paper, we present results validating the ability to detect functional activity using BOSS FMRI. One of the potential advantages of BOSS FMRI is the ability to acquire high-resolution data due to the SNR efficiency of balanced-SSFP. Preliminary high resolution results (1 x 1 x 2 mm/sup 3/) at 1.5 T are presented.

  View details for PubMedID 17271520

• Flexible real-time magnetic resonance imaging framework. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference Santos, J. M., Wright, G. A., Pauly, J. M. 2004; 2: 1048-1051

  Abstract

  The extension of MR imaging to new applications has demonstrated the limitations of the architecture of current real-time systems. Traditional real-time implementations provide continuous acquisition of data and modification of basic sequence parameters on the fly. We have extended the concept of real-time MRI by designing a system that drives the examinations from a real-time localizer and then gets reconfigured for different imaging modes. Upon operator request or automatic feedback the system can immediately generate a new pulse sequence or change fundamental aspects of the acquisition such as gradient waveforms excitation pulses and scan planes. This framework has been implemented by connecting a data processing and control workstation to a conventional clinical scanner. Key components on the design of this framework are the data communication and control mechanisms, reconstruction algorithms optimized for real-time and adaptability, flexible user interface and extensible user interaction. In this paper we describe the various components that comprise this system. Some of the applications implemented in this framework include real-time catheter tracking embedded in high frame rate real-time imaging and immediate switching between real-time localizer and high-resolution volume imaging for coronary angiography applications.

  View details for PubMedID 17271862

• Knee cartilage volume with fluctuating equilibrium MRI 9th World Congress of the OsteoArthritis-Research-Society-International Gold, G. E., Hargreaves, B. A., Vasanawala, S. S., Webb, J., Shimakawa, A., Brittain, J. H., Pauly, J. M., Beaulieu, C. F. W B SAUNDERS CO LTD. 2004: S1–S1

  View details for Web of Science ID 000225708200003

• Learned regulation of spatially localized brain activation using real-time fMRI NEUROIMAGE DeCharms, R. C., Christoff, K., Glover, G. H., Pauly, J. M., Whitfield, S., Gabrieli, J. D. 2004; 21 (1): 436-443

  Abstract

  It is not currently known whether subjects can learn to voluntarily control activation in localized regions of their own brain using neuroimaging. Here, we show that subjects were able to learn enhanced voluntary control over task-specific activation in a chosen target region, the somatomotor cortex. During an imagined manual action task, subjects were provided with continuous direction regarding their cognitive processes. Subjects received feedback information about their current level of activation in a target region of interest (ROI) derived using real-time functional magnetic resonance imaging (rtfMRI), and they received automatically-adjusted instructions for the level of activation to achieve. Information was provided both as continously upated graphs and using a simple virtual reality interface that provided an image analog of the level of activation. Through training, subjects achieved an enhancement in their control over brain activation that was anatomically specific to the target ROI, the somatomotor cortex. The enhancement took place when rtfMRI-based training was provided, but not in a control group that received similar training without rtfMRI information, showing that the effect was not due to conventional, practice-based neural plasticity alone. Following training, using cognitive processes alone subjects could volitionally induce fMRI activation in the somatomotor cortex that was comparable in magnitude to the activation observed during actual movement. The trained subjects increased fMRI activation without muscle tensing, and were able to continue to control brain activation even when real-time fMRI information was no longer provided. These results show that rtfMRI information can be used to direct cognitive processes, and that subjects are able to learn volitionally regulate activation in an anatomically-targeted brain region, surpassing the task-driven activation present before training.

  View details for DOI 10.1016/j.neuroimage.2003.08.041

  View details for Web of Science ID 000188597500044

  View details for PubMedID 14741680

• Spiral magnetic resonance coronary angiography - Direct comparison of 1.5 tesla vs. 3 tesla JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE Yang, P. C., Nguyen, P., Shimakawa, A., Brittain, J., Pauly, J., Nishimura, D., Hu, B., McConnell, M. 2004; 6 (4): 877-884

  Abstract

  MR coronary angiography (MRCA) has been demonstrated successfully at 3 Tesla (T). However, the advantages remain unclear. No systematic comparison of MRCA between 1.5 T and 3 T has been performed. Therefore, anatomic coverage, image quality, signal-to-noise ratio (SNR), contrast-to-noise ration (CNR), and susceptibility artifacts were compared in 23 subjects.Identical real-time (RT) and high-resolution (HR) sequences were implemented on the GE 1.5 T (Signa Twinspeed) and 3.0 T (Signa VH/i) whole body systems (GE, Milwaukee, WI). Both scanners were equipped with high-performance gradient systems capable of 40 mT/m peak amplitude and 150 mT/m/ms slew rate. Real-time localization of the coronary arteries was followed by a cardiac-gated, breath-hold HR sequence. Twenty-three subjects were recruited consecutively and underwent both 3 T and 1.5 T MRCA within one week. Coronary coverage based on the number of coronary segments visualized, image quality using a grading scale, SNR, CNR, and presence of susceptibility artifacts were analyzed. A significant improvement in SNR (47%), CNR (30%), and image quality were seen in 3 T. However, a significant increase in susceptibility artifacts was also noted.MRCA at 3 T significantly improves SNR, CNR, and image quality at the expense of susceptibility artifacts. Further optimization of the imaging parameters at 3 T may facilitate clinical implementation of MRCA.

  View details for DOI 10.1081/JCMR.20036180

  View details for PubMedID 15646891

• Real-time imaging of skeletal muscle velocity 9th Annual Meeting of the ISMRM Asakawa, D. S., Nayak, K. S., Blemker, S. S., Delp, S. L., Pauly, J. M., Nishimura, D. G., Gold, G. E. JOHN WILEY & SONS INC. 2003: 734–39

  Abstract

  To test the feasibility of using real-time phase contrast (PC) magnetic resonance imaging (MRI) to track velocities (1-20 cm/second) of skeletal muscle motion.To do this we modified a fast real-time spiral PC pulse sequence to accommodate through-plane velocity encoding in the range of -20 to +20 cm/second. We successfully imaged motion of the biceps brachii and triceps brachii muscles during elbow flexion and extension in seven unimpaired adult subjects using real-time PC MRI.The velocity data demonstrate that the biceps brachii and the triceps brachii, antagonistic muscles, move in opposite directions during elbow flexion and extension with velocity values in the muscle tissue ranging from -10 to +10 cm/second.With further development, real-time PC MRI may provide a means to analyze muscle function in individuals with neurologic or movement disorders who cannot actively complete the repeated motions required for dynamic MRI techniques, such as cine PC MRI, that are more commonly used in musculoskeletal biomechanics applications.

  View details for DOI 10.1002/jmri.10422

  View details for Web of Science ID 000186844200013

  View details for PubMedID 14635159

• Triggered, navigated, multi-baseline method for proton resonance frequency temperature mapping with respiratory motion MAGNETIC RESONANCE IN MEDICINE Vigen, K. K., Daniel, B. L., Pauly, J. M., Butts, K. 2003; 50 (5): 1003-1010

  Abstract

  A technique is presented for the acquisition of temperature maps in the presence of variable respiratory motion using the proton resonance frequency (PRF) shift. The technique uses respiratory triggering, diaphragm position determination with a navigator echo, and the collection of multiple baseline images to generate temperature maps. Laser ablations were performed in an ex vivo liver phantom undergoing variable simulated respiratory motion and in vivo in four porcine livers, demonstrating a reduction of artifacts in the computed temperature maps compared with conventional single baseline techniques, both uncorrected and corrected for motion.

  View details for DOI 10.1002/mrm.10608

  View details for PubMedID 14587011

• Functional brain Imaging using a blood oxygenation sensitive steady state MAGNETIC RESONANCE IN MEDICINE Miller, K. L., Hargreaves, B. A., Lee, J., Ress, D., deCharms, R. C., Pauly, J. M. 2003; 50 (4): 675-683

  Abstract

  Blood oxygenation level dependent (BOLD) functional MRI (fMRI) is an important method for functional neuroimaging that is sensitive to changes in blood oxygenation related to brain activation. While BOLD imaging has good spatial coverage and resolution relative to other neuroimaging methods (such as positron emission tomography (PET)), it has significant limitations relative to other MRI techniques, including poor spatial resolution, low signal levels, limited contrast, and image artifacts. These limitations derive from the coupling of BOLD functional contrast to sources of image degradation. This work presents an alternative method for fMRI that may over-come these limitations by establishing a blood oxygenation sensitive steady-state (BOSS) that inverts the signal from deoxygenated blood relative to the water signal. BOSS fMRI allows the imaging parameters to be optimized independently of the functional contrast, resulting in fewer image artifacts and higher signal-to-noise ratio (SNR). In addition, BOSS fMRI has greater functional contrast than BOLD. BOSS fMRI requires careful shimming and multiple acquisitions to obtain a precise alignment of the magnetization to the SSFP frequency response.

  View details for DOI 10.1002/mrm.10602

  View details for Web of Science ID 000185698000004

  View details for PubMedID 14523951

• Nonlinear phase correction for navigated diffusion imaging MAGNETIC RESONANCE IN MEDICINE Miller, K. L., Pauly, J. M. 2003; 50 (2): 343-353

  Abstract

  Motion during diffusion-weighted imaging (DWI) introduces phase errors that can cause significant artifacts in brain images. One method of correcting these errors uses additional navigator data to measure the phase corruptions. Standard navigator methods correct for rigid-body motion but cannot correct for nonrigid deformations of the brain related to the cardiac cycle. This work derives a generalized reconstruction that corrects for nonrigid motion based on a least-squares formulation. Since this reconstruction has the disadvantage of being computationally expensive, an approximation is presented, called a refocusing reconstruction. The refocusing reconstruction is both efficient and straightforward. Each readout is multiplied in image space by the phase conjugate of the navigator image, and these rephased readouts are then summed. The conditions under which the refocusing reconstruction is sufficient are considered and methods to improve the quality of refocused images are discussed. In particular, synchronization of the acquisition to the cardiac cycle can provide data that is well-conditioned to the refocusing reconstruction without incurring the large time penalty traditionally associated with cardiac gating. These methods are applied to steady-state DWI, a promising pulse sequence that is particularly sensitive to motion-induced phase artifacts. The refocusing reconstruction is shown to significantly improve SS-DWI over standard rigid-body corrections.

  View details for DOI 10.1002/mrm.10531

  View details for Web of Science ID 000184529300015

  View details for PubMedID 12876711

• Spiral magnetic resonance coronary angiography with rapid real-time localization JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Yang, P. C., Meyer, C. H., Terashima, M., Kaji, S., McConnell, M. V., Macovski, A., Pauly, J. M., Nishimura, D. G., Hu, B. S. 2003; 41 (7): 1134-1141

  Abstract

  A spiral high-resolution coronary artery imaging sequence (SH) interfaced with real-time localization system (RT) has been developed. A clinical study of 40 patients suspected of coronary artery disease (CAD) was conducted. Segmented k-space acquisition techniques have dominated magnetic resonance coronary angiography (MRCA) over the last decade. Although a recent multicenter trial using this technique demonstrated encouraging results, the technique was hampered by low specificity. Spiral k-space acquisition had demonstrated several advantages for MRCA. Therefore, a first clinical trial implementing spiral high-resolution coronary imaging sequence with real-time localization (SH-RT) was performed.A clinical study of 40 patients suspected of CAD undergoing X-ray angiography was conducted to analyze the clinical reliability of this novel imaging system. The SH-RT had been designed to exploit the unique capability of two imaging sequences. The RT allowed a rapid localization of the coronary arteries. Then SH achieved multislice acquisition during a short breath-hold with submillimeter resolution. The MRCA data were analyzed for scan time, anatomic coverage, image quality, and accuracy in detecting CAD. In 40 subjects, SH achieved 0.7 to 0.9 mm resolution with 14-heartbeat breath-holds. Excellent or good image quality was achieved in 78% (263/337) of the coronary segments. Blinded consensus reading among three observers generated sensitivity of 76% and specificity of 91% in the detection of CAD compared with X-ray angiography. The MRCA imaging sequence implementing a novel spiral k-space acquisition technique enabled rapid and reliable imaging of the CAD in submillimeter resolution with short breath-holds.

  View details for DOI 10.1016/S0735-1097(03)00079-2

  View details for Web of Science ID 000181968900011

  View details for PubMedID 12679213

• Comparison of new sequences for high-resolution cartilage imaging MAGNETIC RESONANCE IN MEDICINE Hargreaves, B. A., Gold, G. E., Beaulieu, C. F., Vasanawala, S. S., Nishimura, D. G., Pauly, J. M. 2003; 49 (4): 700-709

  Abstract

  The high prevalence of osteoarthritis continues to demand improved accuracy in detecting cartilage injury and monitoring its response to different treatments. MRI is the most accurate noninvasive method of diagnosing cartilage lesions. However, MR imaging of cartilage is limited by scan time, signal-to-noise ratio (SNR), and image contrast. Recently, there has been renewed interest in SNR-efficient imaging sequences for imaging cartilage, including various forms of steady-state free-precession as well as driven-equilibrium imaging. This work compares several of these sequences with existing methods, both theoretically and in normal volunteers. Results show that the new steady-state methods increase SNR-efficiency by as much as 30% and improve cartilage-synovial fluid contrast by a factor of three. Additionally, these methods markedly decrease minimum scan times, while providing 3D coverage without the characteristic blurring seen in fast spin-echo images.

  View details for DOI 10.1002/mrm.10424

  View details for Web of Science ID 000182007200013

  View details for PubMedID 12652541

• Adaptive real-time architecture in magnetic resonance coronary angiography: Clinical study 52nd Annual Scientific Session of the American-College-of-Cardiology Nguyen, P. K., Santos, J., Scott, G., Engvall, J., Wright, G., McConnell, M., Meyer, C., Nishimura, D., Pauly, J., Hu, B., Yang, P. C. ELSEVIER SCIENCE INC. 2003: 468A–469A

  View details for Web of Science ID 000181669502032

• Adaptive real-time imaging in magnetic resonance coronary angiography Clinical Research 2003 Meeting Yang, P., Nguyen, P., Santos, J., Engvall, J., McConnell, M., Scott, G., Wright, G., Nishimura, D., Pauly, J., Hu, B. B C DECKER INC. 2003: S360–S360

  View details for Web of Science ID 000181390700028

• MR imaging of knee cartilage with FEMR SKELETAL RADIOLOGY Vasnawala, S. S., Pauly, J. M., Nishimura, D. G., Gold, G. E. 2002; 31 (10): 574-580

  Abstract

  Fluctuating equilibrium magnetic resonance (FEMR) is a rapid three-dimensional (3D) imaging sequence with high signal-to-noise ratio (SNR). FEMR may be useful for detecting cartilage defects in the knee. At 1.5 T, FEMR uses a TR with odd multiples of 2.2 ms for fat/water separation. With a TR of 6.6 ms, high-resolution 3D imaging of cartilage is possible.The knees of 10 volunteers and two patients were imaged on a GE Signa 1.5 T scanner using an extremity coil. Scans were preceded by a shimming sequence optimizing linear terms. Subjects were imaged with FEMR, proton-density fast spin-echo (PD-FSE), T2-weighted fast spin-echo (T2-FSE), and 3D fat-suppressed spoiled-gradient-recalled echo (3D-SPGR).SNR and contrast-to-noise efficiency measurements for cartilage using FEMR were superior to those using PD-FSE, T2-FSE, and 3D-FS-SPGR. FSE images showed bright synovial fluid with limited cartilage detail. 3D-SPGR had comparable resolution to FEMR but suboptimal cartilage/fluid contrast and longer scan times (8 min versus 2 min). Cartilage surface detail, outlined by bright synovial fluid, was best seen on the FEMR images.FEMR obtains high-resolution 3D images of the entire knee in 2 min with excellent cartilage/fluid contrast. FEMR is sensitive to field inhomogeneity and requires shimming. Surface defects are outlined by bright synovial fluid, and cartilage has higher signal-to-noise efficiency compared with PD-FSE, T2-FSE, and 3D-SPGR techniques.

  View details for DOI 10.1007/s00256-002-0562-4

  View details for Web of Science ID 000178773000003

  View details for PubMedID 12324826

• Short echo time MR spectroscopic imaging of the lung parenchyma JOURNAL OF MAGNETIC RESONANCE IMAGING Gold, G. E., Pauly, J. M., Leung, A. N., Block, W. F., Meyer, C. H., Sze, R., Macovski, A., Stark, P. 2002; 15 (6): 679-684

  Abstract

  To perform short echo time MR spectroscopic imaging of the lung parenchyma on normal volunteers.A short echo time projection-reconstruction spectroscopic imaging sequence was implemented on a commercial 1.5T whole body MRI scanner. Images and spectra of the lung parenchyma were obtained from five normal volunteers. Breath-held spectroscopic imaging was also performed.Spectroscopic imaging of short-T2* species allows visualization of different anatomic structures based upon their frequency shifts. A characteristic peak from the parenchyma was seen at three ppm from water frequency.Short echo time MR spectroscopic imaging of the lung parenchyma was demonstrated in normal volunteers. This method may improve proton imaging of the lungs and add specificity to the diagnosis of pulmonary disease.

  View details for DOI 10.1002/jmri.10113

  View details for Web of Science ID 000175918300008

  View details for PubMedID 12112518

• Rapid evaluation of right ventricular volume and mass without breath-holding using real-time interactive cardiac magnetic resonance imaging system Kaji, S., Yang, P. C., Kerr, A. B., Meyer, C. H., Pauly, J. M., Hu, B. S. ELSEVIER SCIENCE INC. 2002: 368A–369A

  View details for Web of Science ID 000174106701658

• In vivo real-time intravascular MRI JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE Rivas, P. A., Nayak, K. S., Scott, G. C., McConnell, M. V., Kerr, A. B., Nishimura, D. G., Pauly, J. M., Hu, B. S. 2002; 4 (2): 223-232

  Abstract

  The Magnetic resonance imaging (MRI) is an emerging technology for catheter-based imaging and interventions. Real-time MRI is a promising methodfor overcoming catheter and physiologic motion for intravascular imaging.All imaging was performed on a 1.5 T Signa MRI scanner with high-speed gradients. Multiple catheter coils were designed and constructed, including low-profile, stub-matched coils. Coil sensitivity patterns and SNR measurements were compared. Real-time imaging was performed with an interleaved spiral sequence using a dedicated workstation, providing real-time data acquisition, image reconstruction and interactive control and display. Real-time "black-blood" imaging was achieved through incorporation of off-slice saturation pulses. The imaging sequence was tested in a continuous flow phantom and then in vivo in the rabbit aorta using a 2 mm catheter coil.The real-time intravascular imaging sequence achieved 120-440 micron resolution at up to 16 frames per second. Low-profile stub-tuned catheter coils achieved similar SNR to larger traditional coil designs. In the phantom experiments, addition of real-time black-blood saturation pulses effectively suppressed the flow signal and allowed visualization of the phantom wall. In vivo experiments clearly showed real-time intravascular imaging of the rabbit aortic wall with minimal motion artifacts and effective blood signal suppression.Real-time imaging with low-profile coil designs provides significant enhancements to intravascular MRI.

  View details for PubMedID 12074137

• Dualband spectral-spatial RF pulses for prostate MR spectroscopic imaging MAGNETIC RESONANCE IN MEDICINE Schricker, A. A., Pauly, J. M., Kurhanewicz, J., Swanson, M. G., Vigneron, D. B. 2001; 46 (6): 1079-1087

  Abstract

  Although MR spectroscopic imaging (MRSI) of the prostate has demonstrated clinical utility for the staging and monitoring of cancer extent, current acquisition methods are often inadequate in several aspects. Conventional 180 degrees pulses can suffer from chemical shift misregistration, and have high peak-power requirements that can exceed hardware limits in many prostate MRSI studies. Optimal water and lipid suppression are also critical to obtain interpretable spectra. While complete suppression of the periprostatic lipid resonance is desired, controlled partial suppression of water can provide a valuable phase and frequency reference for data analysis and an assessment of experimental success in cases in which all other resonances are undetectable following treatment. In this study, new spectral-spatial RF pulses were developed to negate chemical shift misregistration errors and to provide dualband excitation with partial excitation of the water resonance and full excitation of the metabolites of interest. Optimal phase modulation was also included in the pulse design to provide 40% reduction in peak RF power. Patient studies using the new pulses demonstrated both feasibility and clear benefits in the reliability and applicability of prostate cancer MRSI.

  View details for Web of Science ID 000172432900006

  View details for PubMedID 11746572

• Temperature mapping of frozen tissue using eddy current compensated half excitation RF pulses MAGNETIC RESONANCE IN MEDICINE Wansapura, J. P., Daniel, B. L., Pauly, J., Butts, K. 2001; 46 (5): 985-992

  Abstract

  Cryosurgery has been shown to be an effective therapy for prostate cancer. Temperature monitoring throughout the cryosurgical iceball could dramatically improve efficacy, since end temperatures of at least -40 degrees C are required. The results of this study indicate that MR thermometry based on tissue R(*)(2) has the potential to provide this information. Frozen tissue appears as a complete signal void on conventional MRI. Ultrashort echo times (TEs), achievable with half pulse excitation and a short spiral readout, allow frozen tissue to be imaged and MR characteristics to be measured. However, half pulse excitation is highly sensitive to eddy current distortions of the slice-select gradient. In this work, the effects of eddy currents on the half pulse technique are characterized and methods to overcome these effects are developed. The methods include: 1) eddy current compensated slice-select gradients, and 2) a correction for the phase shift between the first and second half excitations at the center of the slice. The effectiveness of these methods is demonstrated in R(*)(2) maps calculated within the frozen region during cryoablation.

  View details for PubMedID 11675651

• High-resolution real-time MRI for vascular interventions Terashima, M., De la pena-Almageur, E., Nayak, K. S., Yang, P. C., Pauly, J. M., Hu, B. S., McConnell, M. V. LIPPINCOTT WILLIAMS & WILKINS. 2001: 638–38

  View details for Web of Science ID 000171895002995

• High-resolution real-time magnetic resonance imaging for vascular interventions. Terashima, M., De La Pena-Almaguer, E., Nayak, K., Pauly, J. M., Yang, P. C., Hu, B. S., McConnell, M. V. EXCERPTA MEDICA INC. 2001: 89G–89G

  View details for Web of Science ID 000170893600229

• Real-time interactive coronary MRA MAGNETIC RESONANCE IN MEDICINE Nayak, K. S., Pauly, J. M., Yang, P. C., Hu, B. S., Meyer, C. H., Nishimura, D. G. 2001; 46 (3): 430-435

  Abstract

  An interactive real-time imaging system capable of rapid coronary artery imaging is described. High-resolution spiral and circular echo planar trajectories were used to achieve 0.8 x 1.6 mm2 resolution in 135 ms (CEPI) or 1.13 x 1.13 mm2 resolution in 189 ms (spirals), over a 20-cm FOV. Using a sliding window reconstruction, display rates of up to 37 images/sec were achieved. Initial results indicate this technique can perform as a high-quality 2D coronary localizer and with SNR improvement may enable rapid screening of the coronary tree.

  View details for Web of Science ID 000170740300004

  View details for PubMedID 11550232

• Rapid evaluation of left ventricular volume and mass without breath-holding using real-time interactive cardiac magnetic resonance imaging system JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Kaji, S., Yang, P. C., Kerr, A. B., Tang, W. H., Meyer, C. H., Macovski, A., Pauly, J. M., Nishimura, D. G., Hu, B. S. 2001; 38 (2): 527-533

  Abstract

  The purpose of this study was to validate cardiac measurements derived from real-time cardiac magnetic resonance imaging (MRI) as compared with well-validated conventional cine MRI.Although cardiac MRI provides accurate assessment of left ventricular (LV) volume and mass, most techniques have been relatively slow and required electrocardiogram (ECG) gating over many heart beats. A newly developed real-time MRI system allows continuous real-time dynamic acquisition and display without cardiac gating or breath-holding.Fourteen healthy volunteers and nine patients with heart failure underwent real-time and cine MRI in the standard short-axis orientation with a 1.5T MRI scanner. Nonbreath-holding cine MRI was performed with ECG gating and respiratory compensation. Left ventricular end-diastolic volume (LVEDV), left ventricular endsystolic volume (LVESV), ejection fraction (EF) and LV mass calculated from the images obtained by real-time MRI were compared to those obtained by cine MRI.The total study time including localization for real-time MRI was significantly shorter than cine MRI (8.6 +/- 2.3 vs. 24.7 +/- 3.5 min, p < 0.001). Both imaging techniques yielded good quality images allowing cardiac measurements. The measurements of LVEDV, LVESV, EF and LV mass obtained with real-time MRI showed close correlation with those obtained with cine MRI (LVEDV: r = 0.985, p < 0.001; LVESV: r = 0.994, p < 0.001; EF: r = 0.975, p < 0.001; LV mass: r = 0.977, p < 0.001).Real-time MRI provides accurate measurements of LV volume and mass in a time-efficient manner with respect to image acquisition.

  View details for Web of Science ID 000170205800033

  View details for PubMedID 11499748

• Characterization and reduction of the transient response in steady-state MR imaging MAGNETIC RESONANCE IN MEDICINE Hargreaves, B. A., Vasanawala, S. S., Pauly, J. M., Nishimura, D. G. 2001; 46 (1): 149-158

  Abstract

  Refocused steady-state free precession (SSFP) imaging sequences have recently regained popularity as faster gradient hardware has allowed shorter repetition times, thereby reducing SSFP's sensitivity to off-resonance effects. Although these sequences offer fast scanning with good signal-to-noise efficiency, the "transient response," or time taken to reach a steady-state, can be long compared with the total imaging time, particularly when using 2D sequences. This results in lost imaging time and has made SSFP difficult to use for real-time and cardiac-gated applications. A linear-systems analysis of the steady-state and transient response for general periodic sequences is shown. The analysis is applied to refocused-SSFP sequences to generate a two-stage method of "catalyzing," or speeding up the progression to steady-state by first scaling, then directing the magnetization. This catalyzing method is compared with previous methods in simulations and experimentally. Although the second stage of the method exhibits some sensitivity to B(1) variations, our results show that the transient time can be significantly reduced, allowing imaging in a shorter total scan time. Magn Reson Med 46:149-158, 2001.

  View details for Web of Science ID 000169561000019

  View details for PubMedID 11443721

• Real-time black-blood MRI using spatial presaturation 7th Annual ISMRM Meeting Nayak, K. S., Rivas, P. A., Pauly, J. M., Scott, G. C., Kerr, A. B., Hu, B. S., Nishimura, D. G. JOHN WILEY & SONS INC. 2001: 807–12

  Abstract

  A real-time interactive black-blood imaging system is described. Rapid blood suppression is achieved by exciting and dephasing slabs outside the imaging slice before each imaging excitation. Sharp-profiled radio frequency saturation pulses placed close to the imaging slice provide good blood suppression, even in views containing slow through-plane flow. In vivo results indicate that this technique improves endocardial border definition during systole in real-time cardiac wall-motion studies. Phantom and animal results indicate that this technique nearly eliminates flow artifacts in real-time intravascular studies. J. Magn. Reson. Imaging 2001;13:807-812.

  View details for Web of Science ID 000171296300020

  View details for PubMedID 11329205

• Rapid ventricular assessment using real-time interactive multislice MRI MAGNETIC RESONANCE IN MEDICINE Nayak, K. S., Pauly, J. M., Nishimura, D. G., Hu, B. S. 2001; 45 (3): 371-375

  Abstract

  A multislice real-time imaging technique is described which can provide continuous visualization of the entire left ventricle under resting and stress conditions. Three dynamically adjustable slices containing apical, mid, and base short axis views are imaged 16 times/sec (48 images/sec), with each image providing 3.12 mm resolution over a 20 cm field of view. Initial studies indicate that this technique is useful for the assessment of LV function by providing simultaneous real-time visualization of all 16 wall segments. This technique may also be used for stress LV function and, when used in conjunction with contrast agents, myocardial perfusion imaging. Magn Reson Med 45:371-375, 2001.

  View details for Web of Science ID 000167163800004

  View details for PubMedID 11241692

• Temperature quantitation and mapping of frozen tissue JOURNAL OF MAGNETIC RESONANCE IMAGING Butts, K., Sinclair, J., Daniel, B. L., Wansapura, J., Pauly, J. M. 2001; 13 (1): 99-104

  Abstract

  A method was developed for quantitating the temperature within frozen tissue with the magnetic resonance (MR) parameter R2*. The pulse sequence uses half-pulse excitation and a short spiral readout to achieve echo times as short as 0.2 msec. Fiber-optic temperature sensors were inserted into bovine liver tissue. The tissue was frozen at one end while being held warm at the other end. Once steady state was reached, the parameter R2* was measured. A linear dependence of R2* on temperature was demonstrated. R2* is independent of freeze number and of the orientation of the temperature gradient with respect to the main magnetic field. Feasibility in a canine prostate during cryosurgery is demonstrated. J. Magn. Reson. Imaging 2001;13:99-104.

  View details for Web of Science ID 000171295800016

  View details for PubMedID 11169810

• Real-time interactive multislice MRI: Stress LV function and first pass perfusion Nayak, K. S., Hu, B. S., Pauly, J. M., Putz, E. J., Kerr, A. B., Nishimura, D. G. LIPPINCOTT WILLIAMS & WILKINS. 2000: 687–87

  View details for Web of Science ID 000090072303314

• Real-time interactive coronary MR angiography Nayak, K. S., Pauly, J. M., Hu, B. S., Yang, P. C., Meyer, C. H., Kerr, A. B., Nishimura, D. G. LIPPINCOTT WILLIAMS & WILKINS. 2000: 398–98

  View details for Web of Science ID 000090072301933

• Partial-FOV reconstruction in dynamic spiral imaging MAGNETIC RESONANCE IN MEDICINE Sedarat, H., Kerr, A. B., Pauly, J. M., Nishimura, D. G. 2000; 43 (3): 429-439

  Abstract

  In many applications of dynamic MR imaging, only a portion of the field-of-view (FOV) exhibits considerable variations in time. In such cases, a prior knowledge of the static part of the image allows a partial-FOV reconstruction of the dynamic section using only a fraction of the raw data. This method of reconstruction generally results in higher temporal resolution, because the scan time for partial-FOV data is shorter. The fidelity of this reconstruction technique depends, among other factors, on the accuracy of the prior information of the static section. This information is usually derived from the reconstructed images at previous time frames. This data, however, is normally corrupted by the motion artifact Because the temporal frequency contents of the motion artifact is very similar to that of the dynamic section, a temporal low-pass filter can efficiently remove this artifact from the static data. The bandwidth of the filter can be obtained from the rate of variations inside and outside the dynamic area. In general, when the temporal bandwidth is not spatially uniform, a bank of low-pass filters can provide a proper suppression of the motion artifact outside the dynamic section. This reconstruction technique is adapted for spiral acquisition and is successfully applied to cardiac fluoroscopy, doubling the temporal resolution.

  View details for Web of Science ID 000085559100015

  View details for PubMedID 10725886

• Complete evaluation of left ventricular volume and mass in less than 5 minutes with real-time interactive cardiac magnetic resonance imaging system Kaji, S., Yang, P. C., Kerr, A. B., Meyer, C. H., Pauly, J. M., Hu, B. S. ELSEVIER SCIENCE INC. 2000: 464A–464A

  View details for Web of Science ID 000085209701776

• Real-time color flow MRI 2nd Annual Meeting of the Society-for-Cardiovascular-Magnetic-Resonance Nayak, K. S., Pauly, J. M., Kerr, A. B., Hu, B. S., Nishimura, D. G. JOHN WILEY & SONS INC. 2000: 251–58

  Abstract

  A real-time interactive color flow MRI system capable of rapidly visualizing cardiac and vascular flow is described. Interleaved spiral phase contrast datasets are acquired continuously, while real-time gridding and phase differencing is used to compute density and velocity maps. These maps are then displayed using a color overlay similar to what is used by ultrasound. For cardiac applications, 6 independent images/sec are acquired with in-plane resolution of 2.4 mm over a 20 cm field of view (FOV). Sliding window reconstruction achieves display rates up to 18 images/sec. Appropriate tradeoffs are made for other applications. Flow phantom studies indicate this technique accurately measures velocities up to 2 m/sec, and accurately captures real-time velocity waveforms (comparable to continuous wave ultrasound). In vivo studies indicate this technique is useful for imaging cardiac and vascular flow, particularly valvular regurgitation. Arbitrary scan planes can be quickly localized, and flow measured in any direction.

  View details for Web of Science ID 000084993500012

  View details for PubMedID 10680689

• The real-time interactive 3-D-DVA for robust coronary MRA IEEE TRANSACTIONS ON MEDICAL IMAGING Sachs, T. S., Meyer, C. H., Pauly, J. M., Hu, B. S., Nishimura, D. G., Macovski, A. 2000; 19 (2): 73-79

  Abstract

  A graphical user interface (GUI) has been developed which enables interactive feedback and control to the real-time diminishing variance algorithm (DVA). This interactivity allows the user to set scan parameters, view scan statistics, and view image updates during the course of the scan. In addition, the DVA has been extended to simultaneously reduce motion artifacts in three dimensions using three orthogonal navigators. Preliminary in vivo studies indicate that these improvements to the standard DVA allow for significantly improved consistency and robustness in eliminating respiratory motion artifacts from MR images, particularly when imaging the coronary arteries.

  View details for Web of Science ID 000086614000001

  View details for PubMedID 10784279

• Evaluation of valvular regurgitation: Real-time color flow magnetic resonance imaging compared to echo Rivas, P. A., Nayak, K. S., Kerr, A. B., McConnell, M. V., Yang, P. C., Pauly, J. M., Nishimura, D. G., Hu, B. S. ELSEVIER SCIENCE INC. 2000: 453A–454A

  View details for Web of Science ID 000085209701735

• Linear combination steady-state free precession MRI MAGNETIC RESONANCE IN MEDICINE Vasanawala, S. S., Pauly, J. M., Nishimura, D. G. 2000; 43 (1): 82-90

  Abstract

  A new, fast, spectrally selective steady-state free precession (SSFP) imaging method is presented. Combining k-space data from SSFP sequences with certain phase schedules of radiofrequency excitation pulses permits manipulation of the spectral selectivity of the image. For example, lipid and water can be resolved. The contrast of each image depends on both T1 and T2, and the relative contribution of the two relaxation mechanisms to image contrast can be controlled by adjusting the flip angle. Several potential applications of the technique, referred to as linear combination steady-state free precession (LCSSFP), are demonstrated: fast musculoskeletal, abdominal, angiographic, and brain imaging.

  View details for Web of Science ID 000084538500010

  View details for PubMedID 10642734

• Abstract: real-time interactive MRI for cardiac applications Computer aided surgery PAULY 2000; 5 (2): 133-?

  View details for PubMedID 10862137

• A randomized clinical trial of risk factor modification in 535 healthy women during menopause Kuller, L. H., Simkin-Silverman, L. R., Milas, N. C., Berry, M., Wing, R. R. LIPPINCOTT WILLIAMS & WILKINS. 1999: 522–22

  View details for Web of Science ID 000083417102747

• Real-time interactive cardiac magnetic resonance imaging system with color flow mapping: Assessment of regurgitation severity compared with ultrasound color doppler Rivas, P. A., Nayak, K. S., Kerr, A. B., Nishimura, D., Pauly, J. M., Hu, B. S. LIPPINCOTT WILLIAMS & WILKINS. 1999: 456–56

  View details for Web of Science ID 000083417102400

• Real-time black-blood cardiac MRI Nayak, K. S., Pauly, J. M., Hu, B. S., Kerr, A. B., Nishimura, D. G. LIPPINCOTT WILLIAMS & WILKINS. 1999: 162–62

  View details for Web of Science ID 000083417100841

• Fluctuating equilibrium MRI MAGNETIC RESONANCE IN MEDICINE Vasanawala, S. S., Pauly, J. M., Nishimura, D. G. 1999; 42 (5): 876-883

  Abstract

  A new fast, spectrally selective imaging method called fluctuating equilibrium magnetic resonance is presented. With all gradients refocused over a repetition interval, certain phase schedules of radiofrequency excitation pulses produce an equilibrium magnetization that fluctuates from excitation to excitation, thus permitting simultaneous acquisition of several images with different contrast features. For example, lipid and water images can be rapidly acquired. The effective echo time can be adjusted using the flip angle, thus providing control over the T(2) contribution to the contrast. Several applications of the technique are presented, including fast musculoskeletal, abdominal, breast, and brain imaging, in addition to MR angiography. A technique for combining lipid and water images generated with this sequence for angiography is described and other potential applications are suggested. Magn Reson Med 42:876-883, 1999.

  View details for Web of Science ID 000083447900006

  View details for PubMedID 10542345

• MR imaging of articular cartilage using driven equilibrium Scientific Meeting of the International-Society-for-Magnetic-Resonance-in-Medicine Hargreaves, B. A., Gold, G. E., Lang, P. K., Conolly, S. M., Pauly, J. M., Bergman, G., Vandevenne, J., Nishimura, D. G. JOHN WILEY & SONS INC. 1999: 695–703

  Abstract

  The high incidence of osteoarthritis and the recent advent of several new surgical and non-surgical treatment approaches have motivated the development of quantitative techniques to assess cartilage loss. Although magnetic resonance (MR) imaging is the most accurate non-invasive diagnostic modality for evaluating articular cartilage, improvements in spatial resolution, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) would be valuable. Cartilage presents an imaging challenge due to its short T(2) relaxation time and its low water content compared with surrounding materials. Current methods sacrifice cartilage signal brightness for contrast between cartilage and surrounding tissue such as bone, bone marrow, and joint fluid. A new technique for imaging articular cartilage uses driven equilibrium Fourier transform (DEFT), a method of enhancing signal strength without waiting for full T(1) recovery. Compared with other methods, DEFT imaging provides a good combination of bright cartilage and high contrast between cartilage and surrounding tissue. Both theoretical predictions and images show that DEFT is a valuable method for imaging articular cartilage when compared with spoiled gradient-recalled acquisition in the steady state (SPGR) or fast spin echo (FSE). The cartilage SNR for DEFT is as high as that of either FSE or SPGR, while the cartilage-synovial fluid CNR of DEFT is as much as four times greater than that of FSE or SPGR. Implemented as a three-dimensional sequence, DEFT can achieve coverage comparable to that of other sequences in a similar scan time. Magn Reson Med 42:695-703, 1999.

  View details for Web of Science ID 000082944400011

  View details for PubMedID 10502758

• Nonsubtractive spiral phase contrast velocity imaging MAGNETIC RESONANCE IN MEDICINE Man, L. C., Pauly, J. M., Nishimura, D. G., Macovski, A. 1999; 42 (4): 704-713

  Abstract

  Phase contrast velocity imaging is a standard method for accurate in vivo flow measurement. One drawback, however, is that it lengthens the scan time (or reduces the achievable temporal resolution) because one has to acquire two or more images with different flow sensitivities and subtract their phases to produce the final velocity image. Without this step, non-flow-related phase variations will give rise to an erroneous, spatially varying background velocity. In this paper, we introduce a novel phase contrast velocity imaging technique that requires the acquisition of only a single image. The idea is to estimate the background phase variation from the flow-encoded image itself and then have it removed, leaving only the flow-related phase to generate a corrected flow image. This technique is sensitive to flow in one direction and requires 50% less scan time than conventional phase contrast velocity imaging. Phantom and in vivo results were obtained and compared with those of the conventional method, demonstrating the new method's effectiveness in measuring flow in various vessels of the body. Magn Reson Med 42:704-713, 1999.

  View details for Web of Science ID 000082944400012

  View details for PubMedID 10502759

• 1999 Gary J. Becker Young Investigator Award. MR-guided transjugular portosystemic shunt placement in a swine model. Journal of vascular and interventional radiology Kee, S. T., Rhee, J. S., Butts, K., Daniel, B., Pauly, J., Kerr, A., O'Sullivan, G. J., Sze, D. Y., Razavi, M. K., Semba, C. P., Herfkens, R. J., Dake, M. D. 1999; 10 (5): 529-535

  Abstract

  To evaluate the performance of portal venous puncture with use of magnetic resonance (MR) guidance, and to place a transjugular intrahepatic portosystemic shunt (TIPS) in a swine model.A study of 12 swine was performed to evaluate the ability of interventional MR imaging to guide portal vein puncture and TIPS placement. Six swine had catheters placed in the right hepatic vein under C-arm fluoroscopy. A nitinol guide wire was left in the vein and the animals were then moved into an open configuration MR imaging unit. A TIPS needle set was used to puncture the portal vein using MR fluoroscopy. The animals were transferred to the C-arm, and venography confirmed portal vein puncture. A follow-up study was performed in six additional swine to place a TIPS using only MR imaging guidance. MR tracking was used to advance a catheter from the right atrium into the inferior vena cava. Puncture of the portal vein was performed and a nitinol stent was placed, bridging the hepatic parenchyma. MR venogram confirmed placement.Successful portal vein puncture was achieved in all animals. The number of punctures required decreased from 12 in the first animal to a single puncture in the last eight swine. A stent was successfully placed across the hepatic tract in all six swine.Real-time MR imaging proved to be a feasible method to guide portal vein puncture and TIPS placement in pigs.

  View details for PubMedID 10357476

• MR-guided transjugular portosystemic shunt placement in a swine model JOURNAL OF VASCULAR AND INTERVENTIONAL RADIOLOGY Kee, S. T., Rhee, J. S., Butts, K., Daniel, B., Pauly, J., Kerr, A., O'Sullivan, G. J., Sze, D. Y., Razavi, M. K., Semba, C. P., Herfkens, R. J., Dake, M. D. 1999; 10 (5): 529-535

  Abstract

  To evaluate the performance of portal venous puncture with use of magnetic resonance (MR) guidance, and to place a transjugular intrahepatic portosystemic shunt (TIPS) in a swine model.A study of 12 swine was performed to evaluate the ability of interventional MR imaging to guide portal vein puncture and TIPS placement. Six swine had catheters placed in the right hepatic vein under C-arm fluoroscopy. A nitinol guide wire was left in the vein and the animals were then moved into an open configuration MR imaging unit. A TIPS needle set was used to puncture the portal vein using MR fluoroscopy. The animals were transferred to the C-arm, and venography confirmed portal vein puncture. A follow-up study was performed in six additional swine to place a TIPS using only MR imaging guidance. MR tracking was used to advance a catheter from the right atrium into the inferior vena cava. Puncture of the portal vein was performed and a nitinol stent was placed, bridging the hepatic parenchyma. MR venogram confirmed placement.Successful portal vein puncture was achieved in all animals. The number of punctures required decreased from 12 in the first animal to a single puncture in the last eight swine. A stent was successfully placed across the hepatic tract in all six swine.Real-time MR imaging proved to be a feasible method to guide portal vein puncture and TIPS placement in pigs.

  View details for Web of Science ID 000084345500001

• Management of biopsy needle artifacts: Techniques for RF-refocused MRI JOURNAL OF MAGNETIC RESONANCE IMAGING Butts, K., Pauly, J. M., Daniel, B. L., Kee, S., Norbash, A. M. 1999; 9 (4): 586-595

  Abstract

  Several methods were investigated to improve the depiction of biopsy needles in radiofrequency (RF)-refocused magnetic resonance imaging. Distortion correction is performed by the use of view angle tilting (VAT): a gradient is employed on the slice-select axis during readout. Needle conspicuity is increased by offsetting the gradient echo from the spin echo and by inverting the 90 degrees RF pulse slice-select gradient. VAT effectively re-registers in-plane shifts. Since this method changes the projection angle through the slice, some structures appear blurred, while other structures appear sharper. VAT does not correct errors in slice selection. Offsetting the spin echo from the gradient echo increases needle conspicuity but can result in a shift in the apparent location of the needle. Inverting the 90 degrees slice-select gradient effectively increases the needle conspicuity with no shift in the needle location. These methods provide an easy and interactive means to manipulate needle artifacts but should be used cautiously.

  View details for Web of Science ID 000080145000013

  View details for PubMedID 10232519

• Ultra-short echo-time 2D time-of-flight MR angiography using a half-pulse excitation MAGNETIC RESONANCE IN MEDICINE Nielsen, H. T., Gold, G. E., Olcott, E. W., Pauly, J. M., Nishimura, D. G. 1999; 41 (3): 591-599

  Abstract

  Flow-related artifacts remain a significant concern for magnetic resonance (MR) angiography because their appearance in angiograms adversely impacts accuracy in evaluation of arterial stenoses. In this paper, a half-pulse excitation scheme for improved two-dimensional time-of-flight (2D TOF) angiography is described. The proposed method eliminates the need for gradient moment nulling (of all orders), providing significant reductions in spin dephasing and consequent artifactual signal loss. Furthermore, because the post-excitation refocusing and flow compensation gradients are obviated, the achievable echo time is dramatically shortened. The half-pulse excitation is employed in conjunction with a fast radial-line acquisition, allowing ultra-short echo times on the order of 250-300 microsec. Radial-line acquisition methods also provide additional benefits for flow imaging: effective mitigation of pulsatile flow artifacts, full k-space coverage, and decreased scan times. The half-pulse excitation/radial-line sequence demonstrated improved performance in initial clinical evaluations of the carotid bifurcation when compared with a conventional 2D TOF sequence.

  View details for Web of Science ID 000079317800023

  View details for PubMedID 10204884

• Real-time interactive MRI for cardiac applications International Symposium on Ultrafast Magnetic Resonance Imaging in Medicine (ISUM 99) Pauly, J., Kerr, A., Meyer, C., Nayak, K., Hu, B., Yang, P., Nishimura, D., Macovski, A. ELSEVIER SCIENCE BV. 1999: 119–123

  View details for Web of Science ID 000085322100017

• New real-time interactive cardiac magnetic resonance imaging system complements echocardiography JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Yang, P. C., Kerr, A. B., Liu, A. C., Liang, D. H., Hardy, C., Meyer, C. H., Macovski, A., Pauly, J. M., Hu, B. S. 1998; 32 (7): 2049-2056

  Abstract

  We conducted an initial clinical trial of a newly developed cardiac magnetic resonance imaging (CMRI) system. We evaluated left ventricular (LV) function in 85 patients to compare the clinical utility of the CMRI system with echocardiography, the current noninvasive gold standard.Conventional CMRI systems require cardiac-gating and respiratory compensation to synthesize a single image from data acquired over multiple cardiac cycles. In contrast, the new CMRI system allows continuous real-time dynamic acquisition and display of any scan plane at 16 images/s without the need for cardiac gating or breath-holding.A conventional 1.5T Signa MRI Scanner (GE, Milwaukee, Wisconsin) was modified by the addition of an interactive workstation and a bus adapter. The new CMRI system underwent clinical trial by testing its ability to evaluate global and regional LV function. The first group (A) consisted of 31 patients with acceptable echocardiography image quality. The second group (B) consisted of 31 patients with suboptimal echocardiography image quality. The third group (C) consisted of 29 patients with severe lung disease or congenital cardiac malformation who frequently have suboptimal echo study. Two independent observers scored wall motion and image quality using the standard 16-segment model and rank-order analysis.CMRI evaluation was complete in less than 15 min. In group A, no significant difference was found between ECHO and CMRI studies (p = NS). In group B, adequate visualization of wall segments was obtained 38% of the time using ECHO and 97% of the time using CMRI (p < 0.0001). When grouped into coronary segments, adequate visualization of at least one segment occurred in 18 of 30 patients (60%) with ECHO and in all 30 patients (100%) with CMRI (p < 0.0001). In group C, adequate visualization of the wall segments was obtained in 58% (CI 0.53-0.62) of the time using echocardiography and 99.7% (CI 0.99-1.0) of the time using CMRI (p < 0.0001).The new CMRI system provides clinically reliable evaluation of LV function and complements suboptimal echocardiography. In comparison with the conventional CMRI, the new CMRI system significantly reduces scan time, patient discomfort and associated cost.

  View details for Web of Science ID 000077396200039

  View details for PubMedID 9857892

• Design of practical T-2-selective RF excitation (TELEX) pulses MAGNETIC RESONANCE IN MEDICINE Sussman, M. S., Pauly, J. M., Wright, G. A. 1998; 40 (6): 890-899

  Abstract

  Traditional T2-based imaging techniques are geared toward imaging long-T2 species. Traditional techniques are, therefore, not optimal in clinical situations where the information of interest lies in the short-T2 species. T2-selective RF excitation (TELEX) is a technique for obtaining a T2-based contrast that highlights short-T2 values while suppressing long-T2 values-opposite to traditional T2 contrast. Previously, TELEX has been demonstrated qualitatively to highlight only very short-T2 values (T2 approximately 0.001 s). When applied to longer T2 values (T2 > or = 0.01 s), TELEX becomes sensitive to deltaB0 non-uniformities. This restricts its application to problems in which the T2 of interest is very short. In this study, TELEX is characterized quantitatively. Furthermore, a bandwidth broadening scheme is developed that reduces the deltaB0 sensitivity of TELEX. This permits the technique to be applied to longer T2 values. The capabilities and limitations of a practical implementation of TELEX are discussed.

  View details for Web of Science ID 000077148000014

  View details for PubMedID 9840834

• Magnetic resonance imaging of knee cartilage repair. Topics in magnetic resonance imaging Gold, G. E., Bergman, A. G., Pauly, J. M., Lang, P., Butts, R. K., Beaulieu, C. F., Hargreaves, B., Frank, L., Boutin, R. D., Macovski, A., Resnick, D. 1998; 9 (6): 377-392

  Abstract

  Cartilage injury resulting in osteoarthritis is a frequent cause of disability in young people. Osteoarthritis, based on either cartilage injury or degeneration, is a leading cause of disability in the United States. Over the last several decades, much progress has been made in understanding cartilage injury and repair. Magnetic resonance (MR) imaging, with its unique ability to noninvasively image and characterize soft tissue, has shown promise in assessment of cartilage integrity. In addition to standard MR imaging methods, MR imaging contrast mechanisms under development may reveal detailed information regarding the physiology and morphology of cartilage. MR imaging will play a crucial role in assessing the success or failure of therapies for cartilage injury and degeneration.

  View details for PubMedID 9894740

• Feasibility study of lactate imaging of head and neck tumors NMR IN BIOMEDICINE Adalsteinsson, E., Spielman, D. M., Pauly, J. M., Terris, D. J., Sommer, G., Macovski, A. 1998; 11 (7): 360-369

  Abstract

  A proton spectroscopic imaging sequence was used to investigate the feasibility of lactate imaging in head and neck tumors. The sequence employs a two-shot lactate editing method with inversion recovery for additional lipid suppression, and a restricted field of view to suppress motion artifacts. Variations in acquisition parameters and two different receive coils were investigated on twelve patients. Elevated lactate was detected in three patients, no lactate was observed in seven patients, and two studies were inconclusive because of severe motion or inhomogeneity artifacts. Best results were obtained with an anterior/posterior neck coil at a 288 ms echo time (TE).

  View details for Web of Science ID 000077335700005

  View details for PubMedID 9859942

• Real-time intravascular magnetic resonance imaging system Hu, B. S., Scott, G. C., Meyer, C. H., Pauly, J. M., Nishimura, D. G., Macovski, A. LIPPINCOTT WILLIAMS & WILKINS. 1998: 857–57

  View details for Web of Science ID 000076594404506

• Real-time cardiac MRI with color flow mapping Nayak, K. S., Kerr, A. B., Hu, B. S., Pauly, J. M., Nishimura, D. G. LIPPINCOTT WILLIAMS & WILKINS. 1998: 513–13

  View details for Web of Science ID 000076594402722

• One-shot spatially resolved velocity imaging MAGNETIC RESONANCE IN MEDICINE Pat, G. T., Pauly, J. M., Hu, B. S., Nishimura, D. G. 1998; 40 (4): 603-613

  Abstract

  For quantitative velocity measurement, we have developed a technique that acquires full velocity spectra without cardiac gating. After a cylindrical excitation restricts imaging to one spatial dimension, data are acquired while an oscillating gradient is played out. After each excitation, an image of velocity versus spatial location is obtained. For a given spatial location, a series of these images can be used to form an image of velocity versus time. Acquisition times are much shorter than for phase-contrast imaging or Fourier-encoded velocity imaging, obviating the need for cardiac gating. Although a two-shot version of this technique has been presented previously, we have developed a one-shot version that offers higher temporal resolution for a given velocity resolution and superior off-resonance properties.

  View details for Web of Science ID 000076080900012

  View details for PubMedID 9771577

• Interactive coronary MRI 5th Annual Meeting of the International-Society-of-Magnetic-Resonance-in-Medicine Hardy, C. J., Darrow, R. D., Pauly, J. M., Kerr, A. B., Dumoulin, C. L., Hu, B. S., Martin, K. M. JOHN WILEY & SONS INC. 1998: 105–11

  Abstract

  The acquisition of complete three-dimensional (3D), segmented gradient-echo data sets to visualize the coronary arteries can be both time consuming and sensitive to motion, even with use of multiple breath-holding or respiratory gating. An alternate hybrid approach is demonstrated here, in which real-time interactive imaging is first used to locate an optimal oblique coronary scan plane. Then, a limited number of contiguous slices are acquired around that plane within a breath-hold with use of two-dimensional (2D) segmented gradient-echo imaging. Dual inversion nulling is used to suppress fat and myocardium. Finally, if needed, a limited reformat of the data is performed to produce images from relatively long sections of the coronaries. This approach yields relatively rapid visualization of portions of the coronary tree. Several different methods are compared for interactively moving the scan plane.

  View details for Web of Science ID 000074302000014

  View details for PubMedID 9660560

• MR imaging of articular cartilage of the knee: New methods using ultrashort TEs AMERICAN JOURNAL OF ROENTGENOLOGY Gold, G. E., Thedens, D., Pauly, J. M., Fechner, K. P., Bergman, G., Beaulieu, C. F., Macovski, A. 1998; 170 (5): 1223-1226

  View details for Web of Science ID 000073257300016

  View details for PubMedID 9574589

• New real-time interactive cardiac magnetic resonance imaging system Yang, P., Kerr, A., Liu, A., Liang, D. H., Hardy, C., Meyer, C., Macovski, A., Pauly, J., Hu, B. ELSEVIER SCIENCE INC. 1998: 3A–4A

  View details for Web of Science ID 000071920600012

• Isotropic diffusion-weighted and spiral-navigated interleaved EPI for routine imaging of acute stroke MAGNETIC RESONANCE IN MEDICINE Butts, K., Pauly, J., deCrespigny, A., Moseley, M. 1997; 38 (5): 741-749

  Abstract

  An interleaved echo-planar imaging (EPI) technique is presented for the rapid acquisition of isotropic diffusion-weighted images of stroke patients. Sixteen isotropic diffusion-weighted images at three b values are acquired in less than 3 min. A spiral navigator echo is used to measure the constant and linear phase shifts across the head in both the x and y directions which result from motion during the isotropic diffusion- sensitizing gradients. The measured k-space errors are corrected during a gridding reconstruction. The gridding kernel has a constant width in kx and a variable width in ky which eliminates variable data-density ghosts. The resulting isotropic diffusion-weighted images have excellent lesion-to-normal brain contrast, very good spatial resolution, and little sensitivity to susceptibility effects in the base of the brain. Examples of diffusion-weighted images and ADC maps from several stroke patients are shown.

  View details for Web of Science ID A1997YD91100009

  View details for PubMedID 9358448

• Real-time interactive cardiac MRI examination should be considered for routine clinical evaluation of left ventricular function in select groups of patients Yang, P. C., Kerr, A. B., Liu, A. C., Liang, D. H., Meyer, C. H., Pitlick, P. T., Macovski, A., Pauly, J. M., Hu, B. S. LIPPINCOTT WILLIAMS & WILKINS. 1997: 1049–49

  View details for Web of Science ID A1997YC88001047

• High resolution magnetic resonance coronary angiography with real-time interactive localization Meyer, C. H., Hu, B. S., Kerr, A. B., Pauly, J. M., Macovski, A., Nishimura, D. G. LIPPINCOTT WILLIAMS & WILKINS. 1997: 1377–77

  View details for Web of Science ID A1997YC88000731

• Real-time interactive MRI on a conventional scanner MAGNETIC RESONANCE IN MEDICINE Kerr, A. B., Pauly, J. M., Hu, B. S., Li, K. C., Hardy, C. J., Meyer, C. H., Macovski, A., Nishimura, D. G. 1997; 38 (3): 355-367

  Abstract

  A real-time interactive MRI system capable of localizing coronary arteries and imaging arrhythmic hearts in real-time is described. Non-2DFT acquisition strategies such as spiral-interleaf, spiral-ring, and circular echo-planar imaging provide short scan times on a conventional scanner. Real-time gridding reconstruction at 8-20 images/s is achieved by distributing the reconstruction on general-purpose UNIX workstations. An X-windows application provides interactive control. A six-interleaf spiral sequence is used for cardiac imaging and can acquire six images/s. A sliding window reconstruction achieves display rates of 16-20 images/s. This allows cardiac images to be acquired in real-time, with minimal motion and flow artifacts, and without breath holding or cardiac gating. Abdominal images are acquired at over 2.5 images/s with spiral-ring or circular echo-planar sequences. Reconstruction rates are 8-10 images/s. Rapid localization in the abdomen is demonstrated with the spiral-ring acquisition, whereas peristaltic motion in the small bowel is well visualized using the circular echo-planar sequence.

  View details for Web of Science ID A1997XW16200002

  View details for PubMedID 9339436

• Consistent fat suppression with compensated spectral-spatial pulses MAGNETIC RESONANCE IN MEDICINE Block, W., Pauly, J., Kerr, A., Nishimura, D. 1997; 38 (2): 198-206

  Abstract

  Reliable fat suppression is especially important with fast imaging techniques such as echo-planar (EPI), spiral, and fast spin-echo (FSE) T2-weighted imaging. Spectral-spatial excitation has a number of advantages over spectrally selective presaturation techniques, including better resilience to B0 and B1 inhomogeneity. In this paper, a FSE sequence using a spectral-spatial excitation pulse for superior fat suppression is presented. Previous problems maintaining the CPMG condition are solved using simple methods to accurately program radio-frequency (RF) phase. Next an analysis shows how B0 eddy currents can reduce fat suppression effectiveness for spectral-spatial pulses designed for conventional gradient systems. Three methods to compensate for the degradation are provided. Both the causes of the degradation and the compensation techniques apply equally to gradient-recalled applications using these pulses. These problems do not apply to pulses designed for high-speed gradient systems. The spectral-spatial FSE sequence delivers clinically lower fat signal with better uniformity than spectrally selective pre-saturation techniques.

  View details for Web of Science ID A1997XN62100006

  View details for PubMedID 9256098

• MRI using piecewise-linear spiral trajectory MAGNETIC RESONANCE IN MEDICINE Liao, J. R., Pauly, J. M., Pelc, N. J. 1997; 38 (2): 246-252

  Abstract

  A new generation of high power gradient systems which allow much faster MR imaging as well as shorter echo times has recently become available. Some of these high-speed gradient systems impose limits on the percentage of time during which the gradient can change in amplitude (slewing duty cycle). While this limitation may be immaterial to many 2DFT and echo planar imaging methods, a traditional circular spiral trajectory is difficult to use on these systems because its gradient waveforms change during the entire course of the trajectory so that the slewing duty cycle during the readout period is 100%. We describe a piecewise-linear spiral trajectory which is composed of linear segments and rounded corners. This trajectory reduces the slewing duty cycle while maintaining the desirable imaging properties of circular spirals including interleaving by simple gradient rotation. For one representative example, the slewing duty cycle is reduced to 46%. A conventional gridding method was used for image reconstruction, but a new numerical algorithm to calculate the density compensation factor was required. Use of piecewise-linear spiral trajectories reduces the impact imposed by limited gradient slewing duty cycle.

  View details for Web of Science ID A1997XN62100012

  View details for PubMedID 9256104

• Improved solvent suppression and increased spatial excitation bandwidths for three-dimensional PRESS CSI using phase-compensating spectral/spatial spin-echo pulses JOURNAL OF MAGNETIC RESONANCE IMAGING StarLack, J., Vigneron, D. B., Pauly, J., Kurhanewicz, J., Nelson, S. J. 1997; 7 (4): 745-757

  Abstract

  Dual phase-compensating spectral/spatial echo-planar (EP) spin-echo (SE) pulses were incorporated into the point resolved spectroscopy (PRESS) excitation sequence to improve water and lipid suppression for 1H chemical shift imaging (CSI) and to decrease the dependence of the PRESS box location upon chemical shift. The asymmetric EPSE pulses (either minimum or maximum phase in the chemical shift domain) were substituted for the two PRESS SE pulses to yield zero phase spectra. Three different pulses were designed and tested at 1.5 T. Pulse 1, targeted for brain CSI (TE > 85 msec), passed choline to lipid resonances, suppressed water, and rephased the methyl lactate doublet independently of TE. Pulse 2, targeted for general purpose shorter TE PRESS, possessed both high chemical shift and spatial domain bandwidths. Pulse 3, designed for prostate CSI, passed choline to citrate resonances while suppressing lipids and water. The three pulses possessed spatial bandwidths ranging between 3.3 and 5.0 kHz, more than three times higher than that offered by one-dimensional SE pulses of equivalent maximum B1 amplitude. Phantom and in vivo experimental results demonstrated that, for EPSE pulses 1 and 2, suppression factors higher than 10(4) were achieved. The increased spatial bandwidths resulted in less contamination by signals from outside the designated PRESS excited region and a significant improvement in the uniformity of metabolite intensities for voxels located near edges of the PRESS box.

  View details for Web of Science ID A1997XL78100020

  View details for PubMedID 9243397

• Background suppression with multiple inversion recovery nulling: Applications to projective angiography MAGNETIC RESONANCE IN MEDICINE Mani, S., Pauly, J., Conolly, S., Meyer, C., Nishimura, D. 1997; 37 (6): 898-905

  Abstract

  We have developed a technique to accurately null the longitudinal magnetization (Mz) of background material. This suppression involves first saturating the longitudinal magnetization (Mz) of a region, and then applying several nonselective inversions. The inversions are timed relative to the saturation such that Mz is nulled across a broad range of T1 at a predetermined time after the initial saturation. B1 and B0 inhomogeneity, which could lead to inaccurate suppression, are dealt with by the combination of a multiple tip saturation sequence and four adiabatic inversion pulses. The suppression sequence can be used to form projective angiograms by selectively tagging the imaging region with the saturation pulse. After the inversions are played out, a projection taken through the tag region when Mz is nulled will only contain signal from blood that has flown into the region after the saturation. Since only two dimensions are acquired, the technique can acquire gated projection angiograms in reasonable scan times. Representative inflow MIR angiograms of the carotid arteries and renal arteries show excellent background suppression.

  View details for Web of Science ID A1997XB90000014

  View details for PubMedID 9178242

• Improved automatic off-resonance correction without a field map in spiral imaging MAGNETIC RESONANCE IN MEDICINE Man, L. C., Pauly, J. M., Macovski, A. 1997; 37 (6): 906-913

  Abstract

  Non-2DFT k-space readout strategies are useful in fast imaging but prone to blurring when reconstructed off resonance. Field inhomogeneities or susceptibility variations, coupled with a long readout time, are the major sources of this artifact. Correction methods based on a priori off-resonance information such as an acquired field map have been proposed in the literature. An alternative approach estimates the spatially varying off-resonance frequency from the data itself before applying a correction. In this latter approach there is a trade-off between the extent of correction and the chance of increased artifact due to estimation error. This paper introduces an improved algorithm for field map estimation which is both faster and more robust than the existing method. It uses a multi-stage estimation of the field map, starting from a coarse estimate both in frequency and space and proceeds towards higher resolution. The new algorithm is applied to phantom and in vivo images acquired with radial and spiral sequences to give sharper images.

  View details for Web of Science ID A1997XB90000015

  View details for PubMedID 9178243

• Multifrequency interpolation for fast off-resonance correction MAGNETIC RESONANCE IN MEDICINE Man, L. C., Pauly, J. M., Macovski, A. 1997; 37 (5): 785-792

  Abstract

  Field inhomogeneities or susceptibility variations produce blurring in images acquired using non-2DFT k-space readout trajectories. This problem is more pronounced for sequences with long readout times such as spiral imaging. Theoretical and practical correction methods based on an acquired field map have been reported in the past. This paper introduces a new correction method based on the existing concept of frequency segmented correction but which is faster and theoretically more accurate. It consists of reconstructing the data at several frequencies to form a set of base images that are then added together with spatially varying linear coefficients derived from the field map. The new algorithm is applied to phantom and in vivo images acquired with projection reconstruction and spiral sequences, yielding sharply focused images.

  View details for Web of Science ID A1997WV93600020

  View details for PubMedID 9126954

• Short echo time projection reconstruction MR imaging of cartilage: Comparison with fat-suppressed spoiled GRASS and magnetization transfer contrast MR imaging RADIOLOGY Brossmann, J., Frank, L. R., Pauly, J. M., Boutin, R. D., Pedowitz, R. A., Haghighi, P., Resnick, D. 1997; 203 (2): 501-507

  Abstract

  To evaluate short echo time (TE) projection reconstruction magnetic resonance (MR) imaging in the detection of cartilage lesions.Twenty-seven cartilage regions of 10 human patellar specimens were examined with the following MR sequences: short TE projection reconstruction (repetition time msec/TE msec, 400/0.15), fat-suppressed three-dimensional spoiled gradient-recalled acquisition in the steady state (Spoiled GRASS) (50/10, 60 degrees flip angle), and magnetization transfer contrast (MTC) subtraction (400/6). MR findings were correlated with histopathologic grading of the cartilage.For detection of cartilage lesions, sensitivity of projection reconstruction imaging (100%) was significantly greater (P = .03) than that of MTC (62%) but not significantly greater (P > .05) than that of Spoiled GRASS (81%) imaging. Accuracy of projection reconstruction was significantly greater than that of MTC (P = .004) and Spoiled GRASS (P = .03) imaging. Unmasking of collagen fibers was most predictive of abnormal signal intensity of the cartilage with all sequences.In vitro, short TE projection reconstruction MR imaging provides superior delineation of cartilage lesions when compared with two other sequences. On Spoiled GRASS and MTC images, signal intensity of the superficial layer of cartilage is not a reliable sign for surface integrity.

  View details for Web of Science ID A1997WU53200041

  View details for PubMedID 9114112

• RARE spiral T-2-weighted imaging MAGNETIC RESONANCE IN MEDICINE Block, W., Pauly, J., Nishimura, D. 1997; 37 (4): 582-590

  Abstract

  Spiral imaging has a number of advantages for fast imaging, including an efficient use of gradient hardware. However, inhomogeneity -induced blurring is proportional to the data acquisition duration. In this paper, we combine spiral data acquisition with a RARE echo train. This allows a long data acquisition interval per excitation, while limiting the effects of inhomogeneity. Long spiral k-space trajectories are partitioned into smaller, annular ring trajectories. Each of these annular rings is acquired during echoes of a RARE echo train. The RARE refocusing RF pulses periodically refocus off-resonant spins while building a long data acquisition. We describe both T2-weighted single excitation and interleaved RARE spiral sequences. A typical sequence acquires a complete data set in three excitations (32 cm FOV, 192 x 192 matrix). At a TR = 2000 ms, we can average two acquisitions in an easy breath-hold interval. A multifrequency reconstruction algorithm minimizes the effects of any off-resonant spins. Though this algorithm needs a field map, we demonstrate how signal averaging can provide the necessary phase data while increasing SNR. The field map creation causes no scan time penalty and essentially no loss in SNR efficiency. Multiple slice, 14-s breath-hold scans acquired on a conventional gradient system demonstrate the performance.

  View details for Web of Science ID A1997WQ66700015

  View details for PubMedID 9094081

• Reduction of motion artifacts in cine MRI using variable-density spiral trajectories MAGNETIC RESONANCE IN MEDICINE Liao, J. R., Pauly, J. M., Brosnan, T. J., Pelc, N. J. 1997; 37 (4): 569-575

  Abstract

  Dynamic cardiac imaging in MRI is a very challenging task. To obtain high spatial resolution, temporal resolution, and signal-to-noise ratio (SNR), single-shot imaging is not sufficient. Use of multishot techniques resolves this problem but can cause motion artifacts because of data inconsistencies between views. Motion artifacts can be reduced by signal averaging at some cost in increased scan time. However, for the same increase in scan time, other techniques can be more effective than simple averaging in reducing the artifacts. If most of the energy of the inconsistencies is limited to a certain region of kappa-space, increased sampling density (oversampling) in this region can be especially effective in reducing motion artifacts. In this work, several variable-density spiral trajectories are designed and tested. Their efficiencies for artifact reduction are evaluated in computer simulations and in scans of normal volunteers. The SNR compromise of these trajectories is also investigated. The authors conclude that variable-density spiral trajectories can effectively reduce motion artifacts with a small loss in SNR as compared with a uniform density counterpart.

  View details for Web of Science ID A1997WQ66700013

  View details for PubMedID 9094079

• Reducing flow artifacts in echo-planar imaging MAGNETIC RESONANCE IN MEDICINE Pat, G. T., Meyer, C. H., Pauly, J. M., Nishimura, D. G. 1997; 37 (3): 436-447

  Abstract

  Echo-planar imaging (EPI) is very susceptible to flow artifacts. Two ways to improve its flow properties are presented. First, "partial flyback" is proposed to reduce artifacts arising from flow in the readout direction. Near the center of k-space, only the even echoes of the EPI echo-train are used. Partial flyback is shown to improve the readout-flow properties at the expense of a slight worsening of the phase-encode flow and off-resonance properties. We recommend that the flyback region acquire 95% of the energy in k-space. Second, "inside-out" EPI is used to reduce artifacts arising from flow in the phase-encode direction. Data collection begins at the center of k-space, with separate interleaves to acquire the top and bottom, halves of k-space. Partial flyback is combined with partial-Fourier EPI and inside-out EPI. Partial-flyback inside-out EPI has worse off-resonance properties than partial-flyback partial-Fourier EPI but demonstrates better flow properties and does not require partial k-space reconstruction.

  View details for Web of Science ID A1997WJ66400018

  View details for PubMedID 9055235

• New real-time interactive cardiac magnetic resonance imaging system is useful in subjects with suboptimal echocardiographic studies Yang, P., Kerr, A., Liu, A., Pauly, J., Hardy, C., Meyer, C., Macovski, A., Hu, B. ELSEVIER SCIENCE INC. 1997: 7595–95

  View details for Web of Science ID A1997WF76100910

• Angiographic imaging with 2D RF pulses MAGNETIC RESONANCE IN MEDICINE Alley, M. T., Pauly, J. M., Sommer, F. G., Pelc, N. J. 1997; 37 (2): 260-267

  Abstract

  Magnetic resonance angiography (MRA) was performed by using RF pulses designed to excite a limited spatial extent in two orthogonal directions. The restriction in the second spatial dimension can be used to increase inflow enhancement and to improve small field-of-view imaging. A rectangular excitation was produced with an "echo-planar" k-space trajectory and a sinc-modulated RF waveform. In vivo images have demonstrated that vessels are more clearly delineated with the two-dimensional excitation. Aliasing artifacts in small field-of-view imaging are significantly reduced, although in some cases complete elimination is not possible due to the nature of the gradient trajectory.

  View details for Web of Science ID A1997WD27200016

  View details for PubMedID 9001151

• Diffusion-weighted interleaved echo-planar imaging with a pair of orthogonal navigator echoes MAGNETIC RESONANCE IN MEDICINE Butts, K., deCrespigny, A., Pauly, J. M., Moseley, M. 1996; 35 (5): 763-770

  Abstract

  This work describes a diffusion-weighted (DW) interleaved echo-planar imaging (IEPI) method for use on either conventional whole-body scanners or scanners equipped with high-speed gradient and receiver hardware. In combination with cardiac gating and motion correction with a pair of orthogonal navigator echoes, the presented method is time-efficient, compensates for patient motions, and is less sensitive to image distortions than single-shot methods. The motion-correction scheme consists of correction for constant and linear phase terms found from the orthogonal navigator echoes. The correction for the linear phase term in the phase-encode direction includes gridding the data to the Cartesian grid. The DW IEPI was used to image a phantom rotating about the slice-select direction, and motion correction was performed to eliminate ghost artifacts arising from motion in either the readout- or phase-encoding directions. DW IEPI with motion correction was performed on a normal volunteer and on a patient with a 26-day-old region of ischemia over much of the right hemisphere.

  View details for Web of Science ID A1996UJ17500017

  View details for PubMedID 8722828

• Decomposition of inflow and blood oxygen level-dependent (BOLD) effects with dual-echo spiral gradient-recalled echo (GRE) fMRI MAGNETIC RESONANCE IN MEDICINE Glover, G. H., Lemieux, S. K., Drangova, M., Pauly, J. M. 1996; 35 (3): 299-308

  Abstract

  Image contrast with gradient-recalled echo sequences (GRE) used for fMRI can have both blood oxygen level-dependent (BOLD) and inflow components, and the latter is often undesirable. A dual-echo technique can be used to differentiate these mechanisms, because modulation of signal from inflow is common to both echoes, whereas susceptibility and diffusion-related signal losses are larger in the second echo. An efficient dual-echo interleaved spiral sequence was developed for use with a conventional scanner. It uses a k-space trajectory that spirals out from the origin while the first echo is collected, then spirals back in while collecting the second echo. Decomposition of the data provides separate images of the inflow and T2-weighted components. Results demonstrate the decomposition with phantom experiments and with photic stimulation in normal volunteers.

  View details for Web of Science ID A1996TX77500003

  View details for PubMedID 8699940

• MR SPECTROSCOPIC IMAGING OF COLLAGEN - TENDONS AND KNEE MENISCI MAGNETIC RESONANCE IN MEDICINE Gold, G. E., Pauly, J. M., Macovski, A., Herfkens, R. J. 1995; 34 (5): 647-654

  Abstract

  Water molecules associated with collagen have short transverse (T2) relaxation times. Projection-reconstruction techniques are able to achieve an echo time (TE) much shorter than conventional techniques, allowing imaging of tissues with T2 < 5 ms. Using these techniques, a conventional 1.5-T MRI human imaging system can directly image collagen-associated water from knee menisci and tendons in normal volunteers and patients. Long-T2 suppression improves the contrast between these structures and the surrounding tissue with long-T2 relaxation times. Spectroscopic imaging provides improved lipid/water registration and information about chemical composition and relaxation times. Direct imaging of tendons and menisci may provide more information about these structures and provide a new way to assess both injury and repair.

  View details for Web of Science ID A1995TD42800001

  View details for PubMedID 8544684

• SPIRAL IMAGING ON A SMALL-BORE SYSTEM AT 4.7T MAGNETIC RESONANCE IN MEDICINE Spielman, D. M., Pauly, J. M. 1995; 34 (4): 580-585

  Abstract

  Spiral imaging has a number of advantages for ultrafast data acquisition. However, implementation on high-field small-bore systems requires carefully addressing the issues of inhomogeneity-induced blurring and gradient hardware constraints. In this paper, spiral imaging on a 40-cm-bore 4.7T CSI Omega System (Bruker Instruments) is discussed. A constant-voltage gradient waveform design algorithm is developed to reduce readout times as well as minimize waveform distortions due to gradient amplifier nonlinearities. Residual errors are then measured and taken into account in the image reconstruction procedure. Multiple spiral interleaves as well as a multifrequency reconstruction algorithm are used to decrease blurring of off-resonance spins. Both phantom and in vivo images demonstrate the performance of the resulting pulse sequences.

  View details for Web of Science ID A1995RX75100013

  View details for PubMedID 8524026

• MAGNETIC-RESONANCE FLUOROSCOPY USING SPIRALS WITH VARIABLE SAMPLING DENSITIES MAGNETIC RESONANCE IN MEDICINE Spielman, D. M., Pauly, J. M., Meyer, C. H. 1995; 34 (3): 388-394

  Abstract

  The imaging of dynamic processes in the body is of considerable interest in interventional examinations as well as kinematic studies, and spiral imaging is a fast magnetic resonance imaging technique ideally suited for such fluoroscopic applications. In this manuscript, magnetic resonance fluoroscopy pulse sequences in which interleaved spirals are used to continuously acquire data and reconstruct one movie frame for each repetition time interval are implemented. For many applications, not all of k-space needs to be updated each frame, and nonuniform k-space sampling can be used to exploit this rapid imaging strategy by allowing variable update rates for different spatial frequencies. Using the appropriate reconstruction algorithm, the temporal updating rate for each spatial frequency is effectively proportional to the corresponding k-space sampling density. Results from a motion phantom as well as in in vivo gadolinium diethylenetriaminopentaacetic acid (Gd-DTPA) bolus tracking studies in a rat model demonstrate the high temporal resolution achievable using these techniques as well as the tradeoffs available with nonuniform sampling densities. This paper focuses on the acquisition of real-time dynamic information, and all images presented are reconstructed retrospectively. The issues of real-time data reconstruction and display are not addressed.

  View details for Web of Science ID A1995RR68700015

  View details for PubMedID 7500878

• SHORT TE PHOSPHORUS SPECTROSCOPY USING A SPIN-ECHO PULSE MAGNETIC RESONANCE IN MEDICINE Lim, K. O., Pauly, J., Webb, P., Hurd, R., Macovski, A. 1994; 32 (1): 98-103

  Abstract

  In vivo phosphorus spectroscopy requires very short acquisition delays in order to capture the signal from components with short transverse relaxation times (T2). The echo time typical of standard slice selective spin-echo pulses are too long for this application, so hard pulse, free induction decay (FID) acquisitions have frequently been used instead. With FID, however, there is an interval between the time of coherence and data acquisition (acquisition delay), with resulting baseline distortions. In this paper we describe the design of a new short TE, slice-selective, composite spin-echo pulse with echo times as short as 2.5 ms. With a long TR, fully relaxed, multislice spectra can be collected. This technique will be useful for assessing in vivo, changes in brain phospholipid activity associated with psychiatric and neurological diseases.

  View details for Web of Science ID A1994NT73800012

  View details for PubMedID 8084242

• LOCALIZED REAL-TIME VELOCITY SPECTRA DETERMINATION MAGNETIC RESONANCE IN MEDICINE Hu, B. S., Pauly, J. M., Nishimura, D. G. 1993; 30 (3): 393-398

  Abstract

  The accurate measurement of flow velocity has long been a subject of NMR research. In the field of medical imaging, a variety of techniques primarily based on the principle of Fourier encoding have been described. Due to time constraints, necessary trade-offs exist between spatial versus velocity spectral resolution. In general, either the average velocity of individual pixels is displayed or velocity spectral determinations are made at the cost of spatial localization. The recent development of multidimensional excitation pulses makes spatial localization possible during the excitation phase of the pulse sequences. This approach, coupled with time varying gradient readout, can be used to obtain single-shot localized velocity spectra. Using these concepts, we have obtained in vivo real-time measurements of localized velocity spectra on our clinical imager.

  View details for Web of Science ID A1993LV99700018

  View details for PubMedID 8412614

• SPATIALLY-RESOLVED AND LOCALIZED REAL-TIME VELOCITY DISTRIBUTION MAGNETIC RESONANCE IN MEDICINE Irarrazabal, P., Hu, B. S., Pauly, J. M., Nishimura, D. G. 1993; 30 (2): 207-212

  Abstract

  A technique is presented for collecting the spin velocity distribution as a function of position and time. It uses a multidimensional excitation pulse to select a cylinder, giving localization in two dimensions. Resolution in the third spatial dimension is achieved in the readout. During readout, an oscillating gradient encodes the acquired data in both one spatial dimension (x) and one velocity dimension (v). Two acquisitions (42 ms each) are needed to get a complete coverage of kx--kv space, which makes this technique real-time. The data is interpolated from the nonuniformly sampled kx--kv space to a Cartesian frame with a gridding scheme to take advantage of the Fast Fourier Transform. The technique was successfully applied to phantoms and normal volunteers, giving reasonable real-time measurements of velocity.

  View details for Web of Science ID A1993LP88200008

  View details for PubMedID 8366802

• INCORPORATING LACTATE LIPID DISCRIMINATION INTO A SPECTROSCOPIC IMAGING SEQUENCE MAGNETIC RESONANCE IN MEDICINE Adalsteinsson, E., Spielman, D. M., Wright, G. A., Pauly, J. M., Meyer, C. H., Macovski, A. 1993; 30 (1): 124-130

  Abstract

  A spectroscopic imaging sequence incorporating a two-shot lactate editing method was used in two human brain studies to image lactate and NAA. The subtractive editing method allows separate images of lactate, NAA, and lipids to be collected during a single study with no SNR penalty. The sequence uses a spectral-spatial excitation for slice selection and water suppression, and employs inversion recovery and an echo time of 136 ms for additional lipid suppression.

  View details for Web of Science ID A1993LK91600018

  View details for PubMedID 8371666

• ECHO-PLANAR SPIN-ECHO AND INVERSION PULSES MAGNETIC RESONANCE IN MEDICINE Pauly, J., Spielman, D., Macovski, A. 1993; 29 (6): 776-782

  Abstract

  The echo-planar k-space trajectory can be used as the basis for any two-dimensional selective pulse. The main application is spectral-spatial pulses, which must be based on the echo-planar trajectory. In this paper we show how echo-planar spin-echo (EPSE) pulses may be designed.

  View details for Web of Science ID A1993LF39300008

  View details for PubMedID 8350720

• CHARACTERIZATION OF ATHEROSCLEROSIS WITH A 1.5-T IMAGING-SYSTEM JMRI-JOURNAL OF MAGNETIC RESONANCE IMAGING Gold, G. E., Pauly, J. M., Glover, G. H., Moretto, J. C., Macovski, A., Herfkens, R. J. 1993; 3 (2): 399-407

  Abstract

  It is shown that a conventional 1.5-T magnetic resonance (MR) imaging system can help characterize some of the key components of atherosclerotic plaque ex vivo. Fresh human aorta with atheromata was suspended in solutions of agarose and manganese chloride and heated to body temperature. The specimens were imaged with modified Dixon and projection-reconstruction imaging sequences. The specimens were then examined histologically to obtain direct correlation between images, spectra, and histologic characteristics. The results show that vessel wall and plaque components can be identified by means of their MR characteristics and correlated with their histologic appearance. The authors were able to identify normal vessel wall components, such as adventitial lipids and smooth muscle. They were also able to identify and localize plaque components such as fibrous tissue, calcification, lipids, and possible areas of hemorrhage and hemosiderin deposition.

  View details for Web of Science ID A1993KQ88100013

  View details for PubMedID 8448403

• MAGNETIC-RESONANCE ANGIOGRAPHY WORKSHOP ON CARDIOVASCULAR IMAGING Macovski, A., Hu, B., Meyer, C., Pauly, J., Wright, G., Nishimura, D. G. RAVEN PRESS. 1993: 221–236

  View details for Web of Science ID A1993BY41M00015

• MAGNETIC-RESONANCE-IMAGING OF LUNG PARENCHYMA JOURNAL OF THORACIC IMAGING Bergin, C. J., GLOVER, G. M., Pauly, J. 1993; 8 (1): 12-17

  Abstract

  Imaging of the lungs presents a unique challenge for MR technology. Signal from lung parenchyma is limited by low proton density, the effects of motion and susceptibility, and a multiexponential T2 relaxation time. We have illustrated the use of spin echo and projection reconstruction MR sequences in imaging lung parenchyma, and the use of a GRE sequence in imaging the pulmonary vascular tree.

  View details for Web of Science ID A1993KF43000002

  View details for PubMedID 8418315

• A 3-DIMENSIONAL SPIN-ECHO OR INVERSION PULSE MAGNETIC RESONANCE IN MEDICINE Pauly, J. M., Hu, B. S., Wang, S. J., Nishimura, D. G., Macovski, A. 1993; 29 (1): 2-6

  Abstract

  In theory, multidimensional pulses can be designed to be selective in any number of dimensions. In practice, available gradient power has enforced a limit to two dimensions. We show here that three-dimensional pi pulses are feasible on commercial imaging machines provided that the range of off-resonance frequencies are limited.

  View details for Web of Science ID A1993KJ34900001

  View details for PubMedID 8419739

• PROJECTION RECONSTRUCTION TECHNIQUES FOR REDUCTION OF MOTION EFFECTS IN MRI MAGNETIC RESONANCE IN MEDICINE Glover, G. H., Pauly, J. M. 1992; 28 (2): 275-289

  Abstract

  Projection reconstruction (PR) techniques are shown to have intrinsic advantages over spin-warp (2DFT) methods with respect to diminished artifacts from respiratory motion. The benefits result from (1) portrayal of artifacts as radial streaks, with the amplitude smallest near the moving elements; (2) streak deployment perpendicular to the direction of motion of moving elements and often residing outside the anatomic boundaries of the subject; (3) inherent signal averaging of low spatial frequencies from oversampling of central k-space data. In addition, respiratory-ordered view angle (ROVA) acquisition is found to diminish residual streaking significantly by reducing interview inconsistencies. Comparisons of 2DFT and PR acquisitions are made with and without ROVA. Reconstructions from magnitude-only projections are found to have increased streaks from motion-induced phase shifts.

  View details for Web of Science ID A1992KB92200008

  View details for PubMedID 1461126

• DEBLURRING FOR NON-2D FOURIER-TRANSFORM MAGNETIC-RESONANCE-IMAGING MAGNETIC RESONANCE IN MEDICINE Noll, D. C., Pauly, J. M., Meyer, C. H., Nishimura, D. G., Macovski, A. 1992; 25 (2): 319-333

  Abstract

  For several non-2D Fourier transform imaging methods, off-resonant reconstruction does not just cause geometric distortion, but changes the shape of the point spread function and causes blurring. This effect is well known for projection reconstruction and spiral k-space scanning sequences. We introduce here a method that automatically removes blur introduced by magnetic field inhomogeneity and susceptibility without using a resonant frequency map, making these imaging methods more useful. In this method, the raw data are modulated to several different frequencies and reconstructed to create a series of base images. Determination of degree of blur is done by calculating a focusing measure for each point in each base image and a composite image is then constructed using only the unblurred regions from each base image. This method has been successfully applied to phantom and in vivo images using projection-reconstruction and spiral-scan sequences.

  View details for Web of Science ID A1992HX35600009

  View details for PubMedID 1614315

• MR IMAGING OF LUNG PARENCHYMA - A SOLUTION TO SUSCEPTIBILITY RADIOLOGY Bergin, C. J., Noll, D. C., Pauly, J. M., Glover, G. H., Macovski, A. 1992; 183 (3): 673-676

  Abstract

  The authors have developed a pulse sequence for imaging lung parenchyma with projection reconstruction magnetic resonance (MR) imaging that reduces the effects of motion and susceptibility. In this study, the projection reconstruction technique was further modified by optimizing MR signal frequencies for reconstructing the images. This was done by means of one of two methods. With the first method, a susceptibility map was derived from the raw image data and this map was used to indicate the optimal frequencies for reconstructing the images. The second method of susceptibility correction was a postprocessing technique in which the optimal reconstruction frequencies were selected with use of specific focusing criteria to generate the least blurred image. The effect of using susceptibility map correction on a phantom was demonstrated, and both of these methods were used to improve the visibility of pulmonary structures on images of subjects with normal and abnormal lungs.

  View details for Web of Science ID A1992HV57800017

  View details for PubMedID 1584917

• LIPID-SUPPRESSED SINGLE-SECTION AND MULTISECTION PROTON SPECTROSCOPIC IMAGING OF THE HUMAN BRAIN JOURNAL OF MAGNETIC RESONANCE IMAGING Spielman, D. M., Pauly, J. M., Macovski, A., Glover, G. H., Enzmann, D. R. 1992; 2 (3): 253-262

  Abstract

  Spectroscopic images of the brain have great potential in disease diagnosis and treatment monitoring. Unfortunately, interfering lipid signals from subcutaneous fat and poor water suppression due to magnetic field inhomogeneities can make such images difficult to obtain. A pulse sequence that uses inversion recovery for lipid suppression and a spectral-spatial refocusing pulse for water suppression is introduced. In contrast to methods that eliminate fat signal by restricting the excited volume to lie completely within the brain, inversion-recovery techniques allow imaging of an entire section without such restrictions. In addition, the spectral-spatial pulse was designed to provide water suppression insensitive to a reasonable range of B0 and B1 inhomogeneities. Several data processing algorithms have also been developed and used in conjunction with the new pulse sequence to produce metabolite maps covering large volumes of the human brain. Images from single- and multisection studies demonstrate the performance of these techniques.

  View details for Web of Science ID A1992HV08100001

  View details for PubMedID 1627859

• 2-DIMENSIONAL SELECTIVE ADIABATIC PULSES MAGNETIC RESONANCE IN MEDICINE Conolly, S., Pauly, J., Nishimura, D., Macovski, A. 1992; 24 (2): 302-313

  Abstract

  Using the technique of separable k-space excitation, we have designed a two-dimensional selective adiabatic pulse that inverts magnetization from a square region in the xy plane with insensitivity to RF variations. We also have designed a two-dimensional adiabatic pulse that inverts selectively in frequency and in one spatial dimension. The pulses should be useful for both MR imaging and spectroscopy. We present experimental results to demonstrate that the two-dimensional adiabatic pulses are feasible on commercial MR imaging systems.

  View details for Web of Science ID A1992HM14900010

  View details for PubMedID 1569869

• EFFECTS OF RF AMPLIFIER DISTORTION ON SELECTIVE EXCITATION AND THEIR CORRECTION BY PREWARPING MAGNETIC RESONANCE IN MEDICINE Chan, F., Pauly, J., Macovski, A. 1992; 23 (2): 224-238

  Abstract

  In a magnetic resonance imaging system, an RF power amplifier is employed to boost an RF pulse to sufficient strength to excite the nuclear spins in a subject. The nonideal behavior of this amplifier distorts a selective-excitation pulse, and this distortion in turn degrades the slice profile. We have found two types of nonideal behavior particularly troublesome: nonlinearity and incidental phase modulation. One of their effects is the introduction of an unwanted "skirt" in the out-of-slice region of a slice profile. We present an effective method of correction in which a selective-excitation pulse is prewarped to compensate for the distortion.

  View details for Web of Science ID A1992HD21300003

  View details for PubMedID 1549038

• B-11 IMAGING WITH A 3-DIMENSIONAL RECONSTRUCTION METHOD JMRI-JOURNAL OF MAGNETIC RESONANCE IMAGING Glover, G. H., Pauly, J. M., Bradshaw, K. M. 1992; 2 (1): 47-52

  Abstract

  A three-dimensional projection reconstruction technique is described for imaging boron-11 distributions, with potential application to boron neutron capture therapy. The method samples a spherical volume of k space uniformly to obtain a 32 x 32 x 32 matrix with voxel size of 0.42 cm3. A signal-to-noise ratio (S/N) of 3 was obtained in 8.5 minutes in a phantom containing 75 micrograms/mL of boron in borocaptate sodium (BSH). Images were obtained in a dog after cessation of an intravenous infusion of BSH and again 30 minutes later, with a maximum boron S/N of about 12. Boron levels in the brain dropped about 6%-8% and were more diffusely distributed on the images obtained 30 minutes after BSH infusion.

  View details for Web of Science ID A1992HB35100007

  View details for PubMedID 1623280

• A HOMOGENEITY CORRECTION METHOD FOR MAGNETIC-RESONANCE-IMAGING WITH TIME-VARYING GRADIENTS IEEE TRANSACTIONS ON MEDICAL IMAGING Noll, D. C., Meyer, C. H., Pauly, J. M., Nishimura, D. G., Macovski, A. 1991; 10 (4): 629-637

  Abstract

  When time-varying gradients are used for imaging, the off-resonance behavior does not just cause geometric distortion as is the case with spin-warp imaging, but changes the shape of the impulse response and causes blurring. This effect is well known for projection reconstruction and spiral k-space scanning sequences. The authors introduce a reconstruction and homogeneity correction method to correct for the zeroth order effects of inhomogeneity using prior knowledge of the inhomogeneity. In this method, the data are segmented according to collection time, reconstructed using some fast, linear algorithm, correlated for inhomogeneity, and then superimposed to yield a homogeneity corrected image. This segmented method is compared to a conjugate phase reconstruction in terms of degree of correction and execution time. The authors apply this method to in vivo images using projection-reconstruction and spiral-scan sequences.

  View details for Web of Science ID A1991GW45200018

  View details for PubMedID 18222870

• ON THE NATURE AND REDUCTION OF THE DISPLACEMENT ARTIFACT IN FLOW IMAGES MAGNETIC RESONANCE IN MEDICINE Nishimura, D. G., Jackson, J. I., Pauly, J. M. 1991; 22 (2): 481-492

  Abstract

  In flow-imaging experiments with 2-D Fourier transform sequences, the time difference between phase encoding and readout leads to a potentially misleading displacement artifact. This artifact arises in regions of rapid flow and high shear, and manifests as an intensity distortion in addition to a bulk shift. We have studied methods of mitigating the artifact, including offset-echo acquisition, backward-evolving phase encoding, moment-compensated phase encoding, and projection-reconstruction imaging. Experiments on flow phantoms verified the nature and reduction of this displacement artifact. Of the four methods studied, the projection-reconstruction sequence proved to be the most effective, completely eliminating the artifact.

  View details for Web of Science ID A1991GV21100043

  View details for PubMedID 1812381

• LUNG PARENCHYMA - MAGNETIC-SUSCEPTIBILITY IN MR IMAGING RADIOLOGY Bergin, C. J., Glover, G. H., Pauly, J. M. 1991; 180 (3): 845-848

  Abstract

  Magnetic susceptibility effects in magnetic resonance (MR) imaging of normal lung parenchyma occur because of magnetic-field inhomogeneities induced by the microscopic heterogeneity of the lung. The effects on MR imaging of the lung are loss of signal from intravoxel phase dispersion (measured with T2') and a shift in the macroscopic resonant frequency from that of water toward that of air (delta v). These effects of MR imaging at 1.5 T were quantitated by measuring T2' decay and delta v at different locations in the lungs of two adult volunteers and one excised inflated human lung. The average T2' was 7 msec in the excised inflated specimen and 6.3 msec in normal in vivo lungs. There was a gravitational increase in T2' from nondependent to dependent lung. T2' increased to 35 msec in atelectatic lung tissue and to more than 140 msec in tumor. The macroscopic resonant lung frequency increased to 3.6 ppm more than that of mediastinal muscle. These values are important for developing MR pulse sequences appropriate for imaging lung parenchyma.

  View details for Web of Science ID A1991GB92600045

  View details for PubMedID 1871305

• LUNG PARENCHYMA - PROJECTION RECONSTRUCTION MR-IMAGING RADIOLOGY Bergin, C. J., Pauly, J. M., Macovski, A. 1991; 179 (3): 777-781

  Abstract

  Magnetic resonance (MR) imaging of lung parenchyma is limited by the low proton density and short T2 in the lung as well as the effects of susceptibility and motion. The MR imaging appearance of lung parenchyma was investigated with a pulse sequence that offers some solutions to these problems. This sequence employs projection reconstruction (PR) acquisition gradients and a section-selective excitation pulse designed to eliminate the need to refocus and to allow low-frequency k-space data to be collected with minimal delay. Echo times as short as 50 microseconds can be achieved, producing a proton-density-weighted image. An excised inflated lung specimen and specimens from human subjects with normal lungs (n = 3), pulmonary arteriovenous malformations (n = 1), bronchogenic carcinoma (n = 1), and bullous lung disease with lung metastases (n = 1) were examined. Signal intensity from lung parenchyma and visibility of pulmonary structures were superior on images obtained with the PR MR imaging technique compared with spin-echo images.

  View details for Web of Science ID A1991FM91000039

  View details for PubMedID 2027991

• SPECTROSCOPIC IMAGING WITH MULTIDIMENSIONAL PULSES FOR EXCITATION - SIMPLE MAGNETIC RESONANCE IN MEDICINE Spielman, D., Pauly, J., Macovski, A., ENZMANN, D. 1991; 19 (1): 67-84

  Abstract

  Proton spectroscopy and spectroscopic imaging in the human brain require the elimination of both water and lipid signals. Strong lipid signals from subcutaneous fat are usually eliminated by confining the excited volume to lie wholly within the skull. Water suppression, however, can be difficult due to both B0 and RF inhomogeneities, which are particularly troublesome in imaging experiments where a relatively large region-of-interest (ROI) is typical. In this paper, we discuss the use of multidimensional selective-excitation pulses (e.g., pulses that are simultaneously selective along two axes) to both define the ROI and provide the necessary water suppression. Pulse sequences providing three-dimensional localization along with water suppression that is insensitive to a range of B0 and RF inhomogeneities are described. Spectra and spectroscopic images (voxel volume = 3.4 cc. acquisition time = 38 min) of various 1H metabolites from a patient with an astrocytoma show clear differences between normal and cancerous tissues and demonstrate the ability of these techniques to be used in vivo.

  View details for Web of Science ID A1991FJ08400006

  View details for PubMedID 2046539

• PARAMETER RELATIONS FOR THE SHINNAR-LEROUX SELECTIVE EXCITATION PULSE DESIGN ALGORITHM IEEE TRANSACTIONS ON MEDICAL IMAGING Pauly, J., LEROUX, P., Nishimura, D., Macovski, A. 1991; 10 (1): 53-65

  Abstract

  An overview of the Shinnar-Le Roux (SLR) algorithm is presented. It is shown how the performance of SLR pulses can be very accurately specified analytically. This reveals how to design a pulse that produces a specified slice profile and allows the pulse designer to trade off analytically the parameters describing the pulse performance. Several examples are presented to illustrate the more important tradeoffs. These include linear-phase and minimum- and maximum-phase pulses. Linear-phase pulses can be refocused with a gradient reversal and can be used as spin-echo pulses. Minimum- and maximum-phase pulses have better slice profiles, but cannot be completely refocused.

  View details for Web of Science ID A1991FD82700006

  View details for PubMedID 18222800

• MAGNETIC-RESONANCE RECONSTRUCTION FROM PROJECTIONS USING HALF THE DATA CONF ON MEDICAL IMAGING 5 : IMAGE PHYSICS Noll, D. C., Pauly, J. M., Nishimura, D. G., Macovski, A. SPIE - INT SOC OPTICAL ENGINEERING. 1991: 29–36

  View details for Web of Science ID A1991BT95P00002

• SIMULTANEOUS SPATIAL AND SPECTRAL SELECTIVE EXCITATION MAGNETIC RESONANCE IN MEDICINE Meyer, C. H., Pauly, J. M., Macovski, A., Nishimura, D. G. 1990; 15 (2): 287-304

  Abstract

  Using a k-space interpretation of small-tip excitation, a single excitation pulse has been designed that is simultaneously selective in space and resonant frequency. An analytic expression for the response of this pulse has been derived. The pulse has been implemented on a 1.5-T imaging system. The pulse has been applied to a rapid gradient-echo imaging sequence that forms both water and fat images within a breath-holding interval. These rapid images are free of the chemical shift artifacts at organ boundaries that typically afflict conventional rapid images. The pulse can be applied to a variety of other sequences, such as multislice water/fat sequences and rapid k-space scanning sequences.

  View details for Web of Science ID A1990DT31800010

  View details for PubMedID 2392053

• A LINEAR CLASS OF LARGE-TIP-ANGLE SELECTIVE EXCITATION PULSES JOURNAL OF MAGNETIC RESONANCE Pauly, J., Nishimura, D., Macovski, A. 1989; 82 (3): 571-587

  View details for Web of Science ID A1989U569900012

• A K-SPACE ANALYSIS OF SMALL-TIP-ANGLE EXCITATION JOURNAL OF MAGNETIC RESONANCE Pauly, J., Nishimura, D., Macovski, A. 1989; 81 (1): 43-56

  View details for Web of Science ID A1989T043900003

• CONSIDERATIONS OF MAGNETIC-RESONANCE ANGIOGRAPHY BY SELECTIVE INVERSION RECOVERY MAGNETIC RESONANCE IN MEDICINE Nishimura, D. G., Macovski, A., Pauly, J. M. 1988; 7 (4): 472-484

  Abstract

  In the selective inversion recovery method for projection angiography, upstream blood is tagged by an inversion excitation and then allowed to flow into the imaged region. The subtraction of this first image from a second image acquired without the tagging leaves a signal from only the selectively tagged blood. Pulse sequence design involves consideration of the duration of the blood transit interval, excitation timing and cardiac gating, static material suppression, inversion excitation pulses, and flow compensation. Each of these considerations must be viewed with respect to the particular application. The method has demonstrated potential application to areas such as the carotid arteries, aortic arch, and peripheral vessels.

  View details for Web of Science ID A1988P618700009

  View details for PubMedID 3173062

• CIRCADIAN-STAGE DEPENDENT EFFECTS OF INTERLEUKIN-2 ON [H-3] TDR INCORPORATION INTO DNA IN THE SMALL-INTESTINE OF CD2F1 MICE Scheving, L. A., Tsai, T. H., Feuers, R. J., PAULY, J. E., Scheving, L. E. WILEY-LISS. 1988: A85–A85

  View details for Web of Science ID A1988N096600302

• EFFECT OF EPIDERMAL GROWTH-FACTOR (EGF) AND FASTING ON DNA-SYNTHESIS IN THE SMALL-INTESTINE OF CD2F1 MALE-MICE Scheving, L. E., Tsai, T. H., Scheving, L. A., PAULY, J. E. WILEY-LISS. 1987: A120–A120

  View details for Web of Science ID A1987H180600450

• MR ANGIOGRAPHY BY SELECTIVE INVERSION RECOVERY MAGNETIC RESONANCE IN MEDICINE Nishimura, D. G., Macovski, A., Pauly, J. M., Conolly, S. M. 1987; 4 (2): 193-202

  Abstract

  A modified inversion-recovery sequence is introduced which performs subtraction angiography by varying time-of-flight effects of blood flowing into an imaged slab. The selective 180 degrees excitation inverts different regions between measurements to isolate arterial and/or venous blood. On normal human subjects, high-resolution carotid artery angiograms have been obtained.

  View details for Web of Science ID A1987G074500013

  View details for PubMedID 3561250

• MAGNETIC-RESONANCE ANGIOGRAPHY IEEE TRANSACTIONS ON MEDICAL IMAGING Nishimura, D. G., Macovski, A., Pauly, J. M. 1986; 5 (3): 140-151

  Abstract

  This paper describes several methods for magnetic resonance angiography that create projection images based solely on flowing blood. To both remove static tissue from the image and generate signals from blood, two classes of methods considered are temporal subtraction and cancelling excitation. Temporal subtraction, analogous to digital subtraction angiography with live and mask images, is performed via phase or magnitude differences in blood signals, while cancelling excitation is characterized by its removal of static structures by selectively exciting only flowing material. Means of projection imaging which incorporate these flow-sensitive methods include variations of thick-slice 2-D spin-wrap imaging, line-scan imaging, and volumetric imaging with time-varying gradients.

  View details for Web of Science ID A1986D759300004

  View details for PubMedID 18244000