Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is used to study microvascular structure and tissue perfusion. In DCE-MRI a bolus of gadolinium based contrast agent is injected into the blood stream and spatiotemporal changes induced by the contrast agent flow are estimated from a time series of MRI data. Sufficient time resolution can often only be obtained by using an imaging protocol which produces undersampled data for each image in the time series. This has led to the popularity of compressed sensing based image reconstruction approaches, where all the images in the time series are reconstructed simultaneously, and temporal coupling between the images is introduced into the problem by a sparsity promoting regularization functional. We propose the use of Huber penalty for temporal regularization in DCE-MRI, and compare it to total variation, total generalized variation and smoothness based temporal regularization models. We also study the effect of spatial regularization to the reconstruction and compare the reconstruction accuracy with different temporal resolutions due to varying undersampling. The approaches are tested using simulated and experimental radial golden angle DCE-MRI data from a rat brain specimen. The results indicate that Huber regularization produces similar reconstruction accuracy with the total variation based models, but the computation times are significantly faster.
Dynamic Contrast-enhanced magnetic resonance imaging (DCE-MRI) is a tissue perfusion imaging technique. Some versatile free-breathing DCE-MRI techniques combining compressed sensing (CS) and parallel imaging with golden-angle radial sampling have been developed to improve motion robustness with high spatial and temporal resolution. These methods have demonstrated good diagnostic performance in clinical setting, but the reconstruction quality will degrade at high acceleration rates and overall reconstruction time remains long. In this paper, we proposed a new parallel CS reconstruction model fo…
Summary mean DCE-MRI variables show a clear dependency between signal and noise variance, which can be shown to reduce the effectiveness of difference assessments. Appropriate transformation of these variables supports statistically efficient and robust comparisons. The capabilities of DCE-MRI based descriptions of hepatic colorectal tumour classification was assessed, with regard to their potential for use as imaging biomarkers. Four DCE-MRI parameters were extracted from 102 selected tumour regions. A multi-dimensional statistical distance metric was assessed for the challenging task of comp…
Hand-crafted features extracted from dynamic contrast-enhanced magnetic resonance images (DCE-MRIs) have shown strong predictive abilities in characterization of breast lesions. However, heterogeneity across medical image datasets hinders the generalizability of these features. One of the sources of the heterogeneity is the variation of MR scanner magnet strength, which has a strong influence on image quality, leading to variations in the extracted image features. Thus, statistical decision algorithms need to account for such data heterogeneity. Despite the variations, we hypothesize that ther…
Purpose: To apply tracer kinetic models as temporal constraints during reconstruction of under-sampled dynamic contrast enhanced (DCE) MRI. Methods: A library of concentration v.s time profiles is simulated for a range of physiological kinetic parameters. The library is reduced to a dictionary of temporal bases, where each profile is approximated by a sparse linear combination of the bases. Image reconstruction is formulated as estimation of concentration profiles and sparse model coefficients with a fixed sparsity level. Simulations are performed to evaluate modeling error, and error statisti…
Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow. We present a framew…
Deep transfer learning using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has shown strong predictive power in characterization of breast lesions. However, pretrained convolutional neural networks (CNNs) require 2D inputs, limiting the ability to exploit the rich 4D (volumetric and temporal) image information inherent in DCE-MRI that is clinically valuable for lesion assessment. Training 3D CNNs from scratch, a common method to utilize high-dimensional information in medical images, is computationally expensive and is not best suited for moderately sized healthcare datasets. …
Purpose: To develop a framework to reconstruct large-scale volumetric dynamic MRI from rapid continuous and non-gated acquisitions, with applications to pulmonary and dynamic contrast enhanced (DCE) imaging. Theory and Methods: The problem considered here requires recovering hundred-gigabytes of dynamic volumetric image data from a few gigabytes of k-space data, acquired continuously over several minutes. This reconstruction is vastly under-determined, heavily stressing computing resources as well as memory management and storage. To overcome these challenges, we leverage intrinsic three dimen…
Intra-frame motion blurring, as a major challenge in free-breathing dynamic MRI, can be reduced if high temporal resolution can be achieved. To address this challenge, this work proposes a highly-accelerated 4D (3D+time) real-time MRI framework with sub-second temporal resolution combining standard stack-of-stars golden-angle radial sampling and tailored GRASP-Pro (Golden-angle RAdial Sparse Parallel) reconstruction. Specifically, 4D real-time MRI acquisition is performed continuously without motion gating or sorting. The k-space centers in stack-of-stars radial data are organized to guide est…
Dynamic contrast-enhanced magnetic resonance imaging (DCE- MRI) is a widely used multi-phase technique routinely used in clinical practice. DCE and similar datasets of dynamic medical data tend to contain redundant information on the spatial and temporal components that may not be relevant for detection of the object of interest and result in unnecessarily complex computer models with long training times that may also under-perform at test time due to the abundance of noisy heterogeneous data. This work attempts to increase the training efficacy and performance of deep networks by determining …
In dynamic MRI, sufficient time resolution can often only be obtained using imaging protocols which produce undersampled data for each image in the time series. This has led to the popularity of compressed sensing (CS) based image reconstruction approaches. One of the problems in CS approaches is determining the regularization parameters, which control the balance between data fidelity the spatial and temporal regularization terms. A data-driven approach is proposed for the total variation regularization parameter selection such that the reconstructions yield expected sparsity levels in the re…
Sustainable Deep Learning-Based Breast Lesion Segmentation: Impact of Breast Region Segmentation on Performance
Norwegian University of Science and Technology（挪威科技大学）；More og Romsdal Hospital Trust（默勒-鲁姆斯达尔医院信托基金）；Stavanger University Hospital（斯塔万格大学医院）；The University of Stavanger（斯塔万格大学）；Akershus University Hospital（阿克什胡斯大学医院）；University of Oslo（奥斯陆大学）
Dynamic Contrast-enhanced Magnetic Resonance Imaging (DCE-MRI) is an important tool for detecting subtle kinetic changes in cancerous tissue. Quantitative analysis of DCE-MRI typically involves the convolution of an arterial input function (AIF) with a nonlinear pharmacokinetic model of the contrast agent concentration. Parameters of the kinetic model are biologically meaningful, but the optimization of the non-linear model has significant computational issues. In practice, convergence of the optimization algorithm is not guaranteed and the accuracy of the model fitting may be compromised. To …
Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) is a valuable tool to localize, characterize, and evaluate anomalous prostate tissue. Ultrafast gradient-echo acquisitions of MRI volumes are generated at regular time intervals while the patient receives a paramagnetic contrast agent. The result is a time series where each voxel exhibits a particular behavior of contrast uptake (wash-in) and posterior wash-out. In this work, a segmentation method is proposed that groups together neighboring voxels with similar contrast wash-out responses, using a variant of the region growing Grow…
Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is used to quantify perfusion and vascular permeability. In most cases a bolus arrival time (BAT) delay exists between the arterial input function (AIF) and the contrast agent arrival in the tissue of interest which needs to be estimated. Existing methods for BAT estimation are tailored to tissue concentration curves which have a fast upslope to the peak as frequently observed in patient data. However, they may give poor results for curves that do not have this characteristic shape such as tissue concentration curves of small anima…
Imaging in clinical oncology trials provides a wealth of information that contributes to the drug development process, especially in early phase studies. This paper focuses on kinetic modeling in DCE-MRI, inspired by mixed-effects models that are frequently used in the analysis of clinical trials. Instead of summarizing each scanning session as a single kinetic parameter -- such as median $\ktrans$ across all voxels in the tumor ROI -- we propose to analyze all voxel time courses from all scans and across all subjects simultaneously in a single model. The kinetic parameters from the usual non-…
Robustness of breast lesion segmentation under MRI undersampling improves with k-space-aware deep learning
Institute for AI in Medicine (IKIM), University Hospital Essen（人工智能医学研究所（IKIM），埃森大学医院）；Department of Physics, Technical University Dortmund（物理系，多特蒙德技术大学）；Division of Radiology, German Cancer Research Center (DKFZ)（放射学部，德国癌症研究中心（DKFZ））；Cancer Research Center Cologne Essen (CCCE), University Medicine Essen（科隆埃森癌症研究中心（CCCE），埃森大学医学中心）；RACOON Study Group, Site Essen（RACOON研究组，埃森站点）；German Cancer Consortium (DKTK), Partner Site Essen（德国癌症联合会（DKTK），埃森合作伙伴站点）；Medical Faculty and Faculty of Computer Science, University of Duisburg-Essen（医学系和计算机科学系，杜伊斯堡-埃森大学）
