Radiotherapy Treatment Assessment using DCE-MRI

Abstract

The goal of modern radiotherapy is to precisely deliver a prescribed radiation dose to delineated target volumes that contain a significant amount of tumor cells while sparing the surrounding healthy tissues/organs. Precise delineation of treatment and avoidance volumes is the key for the precision radiation therapy. In recent years, considerable clinical and research efforts have been devoted to integrate MRI into radiotherapy workflow motivated by the superior soft tissue contrast and functional imaging possibility. Dynamic contrast-enhanced MRI (DCE-MRI) is a noninvasive technique that measures properties of tissue microvasculature. Its sensitivity to radiation-induced vascular pharmacokinetic (PK) changes has been preliminary demonstrated. In spite of its great potential, two major challenges have limited DCE-MRI’s clinical application in radiotherapy assessment: the technical limitations of accurate DCE-MRI imaging implementation and the need of novel DCE-MRI data analysis methods for richer functional heterogeneity information.

This study aims at improving current DCE-MRI techniques and developing new DCE-MRI analysis methods for particular radiotherapy assessment. Thus, the study is naturally divided into two parts. The first part focuses on DCE-MRI temporal resolution as one of the key DCE-MRI technical factors, and some improvements regarding DCE-MRI temporal resolution are proposed; the second part explores the potential value of image heterogeneity analysis and multiple PK model combination for therapeutic response assessment, and several novel DCE-MRI data analysis methods are developed.

I. Improvement of DCE-MRI temporal resolution. First, the feasibility of improving DCE-MRI temporal resolution via image undersampling was studied. Specifically, a novel MR image iterative reconstruction algorithm was studied for DCE-MRI reconstruction. This algorithm was built on the recently developed compress sensing (CS) theory. By utilizing a limited k-space acquisition with shorter imaging time, images can be reconstructed in an iterative fashion under the regularization of a newly proposed total generalized variation (TGV) penalty term. In the retrospective study of brain radiosurgery patient DCE-MRI scans under IRB-approval, the clinically obtained image data was selected as reference data, and the simulated accelerated k-space acquisition was generated via undersampling the reference image full k-space with designed sampling grids. Two undersampling strategies were proposed: 1) a radial multi-ray grid with a special angular distribution was adopted to sample each slice of the full k-space; 2) a Cartesian random sampling grid series with spatiotemporal constraints from adjacent frames was adopted to sample the dynamic k-space series at a slice location. Two sets of PK parameters’ maps were generated from the undersampled data and from the fully-sampled data, respectively. Multiple quantitative measurements and statistical studies were performed to evaluate the accuracy of PK maps generated from the undersampled data in reference to the PK maps generated from the fully-sampled data. Results showed that at a simulated acceleration factor of four, PK maps could be faithfully calculated from the DCE images that were reconstructed using undersampled data, and no statistically significant differences were found between the regional PK mean values from undersampled and fully-sampled data sets. DCE-MRI acceleration using the investigated image reconstruction method has been suggested as feasible and promising.

Second, for high temporal resolution DCE-MRI, a new PK model fitting method was developed to solve PK parameters for better calculation accuracy and efficiency. This method is based on a derivative-based deformation of the commonly used Tofts PK model, which is presented as an integrative expression. This method also includes an advanced Kolmogorov-Zurbenko (KZ) filter to remove the potential noise effect in data and solve the PK parameter as a linear problem in matrix format. In the computer simulation study, PK parameters representing typical intracranial values were selected as references to simulated DCE-MRI data for different temporal resolution and different data noise level. Results showed that at both high temporal resolutions (<1s) and clinically feasible temporal resolution (~5s), this new method was able to calculate PK parameters more accurate than the current calculation methods at clinically relevant noise levels; at high temporal resolutions, the calculation efficiency of this new method was superior to current methods in an order of 102. In a retrospective of clinical brain DCE-MRI scans, the PK maps derived from the proposed method were comparable with the results from current methods. Based on these results, it can be concluded that this new method can be used for accurate and efficient PK model fitting for high temporal resolution DCE-MRI.

II. Development of DCE-MRI analysis methods for therapeutic response assessment. This part aims at methodology developments in two approaches. The first one is to develop model-free analysis method for DCE-MRI functional heterogeneity evaluation. This approach is inspired by the rationale that radiotherapy-induced functional change could be heterogeneous across the treatment area. The first effort was spent on a translational investigation of classic fractal dimension theory for DCE-MRI therapeutic response assessment. In a small-animal anti-angiogenesis drug therapy experiment, the randomly assigned treatment/control groups received multiple fraction treatments with one pre-treatment and multiple post-treatment high spatiotemporal DCE-MRI scans. In the post-treatment scan two weeks after the start, the investigated Rényi dimensions of the classic PK rate constant map demonstrated significant differences between the treatment and the control groups; when Rényi dimensions were adopted for treatment/control group classification, the achieved accuracy was higher than the accuracy from using conventional PK parameter statistics. Following this pilot work, two novel texture analysis methods were proposed. First, a new technique called Gray Level Local Power Matrix (GLLPM) was developed. It intends to solve the lack of temporal information and poor calculation efficiency of the commonly used Gray Level Co-Occurrence Matrix (GLCOM) techniques. In the same small animal experiment, the dynamic curves of Haralick texture features derived from the GLLPM had an overall better performance than the corresponding curves derived from current GLCOM techniques in treatment/control separation and classification. The second developed method is dynamic Fractal Signature Dissimilarity (FSD) analysis. Inspired by the classic fractal dimension theory, this method measures the dynamics of tumor heterogeneity during the contrast agent uptake in a quantitative fashion on DCE images. In the small animal experiment mentioned before, the selected parameters from dynamic FSD analysis showed significant differences between treatment/control groups as early as after 1 treatment fraction; in contrast, metrics from conventional PK analysis showed significant differences only after 3 treatment fractions. When using dynamic FSD parameters, the treatment/control group classification after 1st treatment fraction was improved than using conventional PK statistics. These results suggest the promising application of this novel method for capturing early therapeutic response.

The second approach of developing novel DCE-MRI methods is to combine PK information from multiple PK models. Currently, the classic Tofts model or its alternative version has been widely adopted for DCE-MRI analysis as a gold-standard approach for therapeutic response assessment. Previously, a shutter-speed (SS) model was proposed to incorporate transcytolemmal water exchange effect into contrast agent concentration quantification. In spite of richer biological assumption, its application in therapeutic response assessment is limited. It might be intriguing to combine the information from the SS model and from the classic Tofts model to explore potential new biological information for treatment assessment. The feasibility of this idea was investigated in the same small animal experiment. The SS model was compared against the Tofts model for therapeutic response assessment using PK parameter regional mean value comparison. Based on the modeled transcytolemmal water exchange rate, a biological subvolume was proposed and was automatically identified using histogram analysis. Within the biological subvolume, the PK rate constant derived from the SS model were proved to be superior to the one from Tofts model in treatment/control separation and classification. Furthermore, novel biomarkers were designed to integrate PK rate constants from these two models. When being evaluated in the biological subvolume, this biomarker was able to reflect significant treatment/control difference in both post-treatment evaluation. These results confirm the potential value of SS model as well as its combination with Tofts model for therapeutic response assessment.

In summary, this study addressed two problems of DCE-MRI application in radiotherapy assessment. In the first part, a method of accelerating DCE-MRI acquisition for better temporal resolution was investigated, and a novel PK model fitting algorithm was proposed for high temporal resolution DCE-MRI. In the second part, two model-free texture analysis methods and a multiple-model analysis method were developed for DCE-MRI therapeutic response assessment. The presented works could benefit the future DCE-MRI routine clinical application in radiotherapy assessment.

Convex Optimization Algorithms and Statistical Bounds for Learning Structured Models

Thesis (Ph.D.)--University of Washington, 2016-08

Likelihood-Based Inference for Partially Observed Multi-Type Markov Branching Processes

Thesis (Ph.D.)--University of Washington, 2016-08

Tensor Completion for Multidimensional Inverse Problems with Applications to Magnetic Resonance Relaxometry

This thesis deals with tensor completion for the solution of multidimensional inverse problems. We study the problem of reconstructing an approximately low rank tensor from a small number of noisy linear measurements. New recovery guarantees, numerical algorithms, non-uniform sampling strategies, and parameter selection algorithms are developed. We derive a fixed point continuation algorithm for tensor completion and prove its convergence. A restricted isometry property (RIP) based tensor recovery guarantee is proved. Probabilistic recovery guarantees are obtained for sub-Gaussian measurement operators and for measurements obtained by non-uniform sampling from a Parseval tight frame. We show how tensor completion can be used to solve multidimensional inverse problems arising in NMR relaxometry. Algorithms are developed for regularization parameter selection, including accelerated k-fold cross-validation and generalized cross-validation. These methods are validated on experimental and simulated data. We also derive condition number estimates for nonnegative least squares problems. Tensor recovery promises to significantly accelerate N-dimensional NMR relaxometry and related experiments, enabling previously impractical experiments. Our methods could also be applied to other inverse problems arising in machine learning, image processing, signal processing, computer vision, and other fields.

Hierarchical Reconstruction Method for Solving Ill-posed Linear Inverse Problems

We present a detailed analysis of the application of a multi-scale Hierarchical Reconstruction method for solving a family of ill-posed linear inverse problems. When the observations on the unknown quantity of interest and the observation operators are known, these inverse problems are concerned with the recovery of the unknown from its observations. Although the observation operators we consider are linear, they are inevitably ill-posed in various ways. We recall in this context the classical Tikhonov regularization method with a stabilizing function which targets the specific ill-posedness from the observation operators and preserves desired features of the unknown. Having studied the mechanism of the Tikhonov regularization, we propose a multi-scale generalization to the Tikhonov regularization method, so-called the Hierarchical Reconstruction (HR) method. First introduction of the HR method can be traced back to the Hierarchical Decomposition method in Image Processing. The HR method successively extracts information from the previous hierarchical residual to the current hierarchical term at a finer hierarchical scale. As the sum of all the hierarchical terms, the hierarchical sum from the HR method provides an reasonable approximate solution to the unknown, when the observation matrix satisfies certain conditions with specific stabilizing functions. When compared to the Tikhonov regularization method on solving the same inverse problems, the HR method is shown to be able to decrease the total number of iterations, reduce the approximation error, and offer self control of the approximation distance between the hierarchical sum and the unknown, thanks to using a ladder of finitely many hierarchical scales. We report numerical experiments supporting our claims on these advantages the HR method has over the Tikhonov regularization method.

Sparse Signal Representation in Digital and Biological Systems

Theories of sparse signal representation, wherein a signal is decomposed as the sum of a small number of constituent elements, play increasing roles in both mathematical signal processing and neuroscience. This happens despite the differences between signal models in the two domains. After reviewing preliminary material on sparse signal models, I use work on compressed sensing for the electron tomography of biological structures as a target for exploring the efficacy of sparse signal reconstruction in a challenging application domain. My research in this area addresses a topic of keen interest to the biological microscopy community, and has resulted in the development of tomographic reconstruction software which is competitive with the state of the art in its field. Moving from the linear signal domain into the nonlinear dynamics of neural encoding, I explain the sparse coding hypothesis in neuroscience and its relationship with olfaction in locusts. I implement a numerical ODE model of the activity of neural populations responsible for sparse odor coding in locusts as part of a project involving offset spiking in the Kenyon cells. I also explain the validation procedures we have devised to help assess the model's similarity to the biology. The thesis concludes with the development of a new, simplified model of locust olfactory network activity, which seeks with some success to explain statistical properties of the sparse coding processes carried out in the network.

Estimação paramétrica e não-paramétrica em modelos de markov ocultos

In this work we study the Hidden Markov Models with finite as well as general state space. In the finite case, the forward and backward algorithms are considered and the probability of a given observed sequence is computed. Next, we use the EM algorithm to estimate the model parameters. In the general case, the kernel estimators are used and to built a sequence of estimators that converge in L1-norm to the density function of the observable process

Metodi numerici per la ricostruzione di immagini di tomosintesi

La tesi affronta il problema della ricostruzione di immagini di tomosintesi, problema che appartiene alla classe dei problemi inversi mal posti e che necessita di tecniche di regolarizzazione per essere risolto. Nel lavoro svolto sono presenti principalmente due contributi: un'analisi del modello di ricostruzione mediante la regolarizzazione con la norma l1; una valutazione dell'efficienza di alcuni metodi tra quelli che in letteratura costituiscono lo stato dell'arte per quanto riguarda i metodi basati sulla norma l1, ma che sono in genere applicati a problemi di deblurring, dunque non usati per problemi di tomosintesi.

Avaliação do efeito de diferentes concentrações de fotoiniciadores em propriedades mecânicas e na cor de um adesivo dental experimental

O presente trabalho teve por foco prover uma revisão de conceitos relacionados às resinas dentais fotopolimeráveis e, também, analisar como diferentes concentrações de fotoiniciadores de uso comum em odontologia podem influenciar no desempenho mecânico e na cor de resinas dentais. Concentrações de 0,01%, 0,10%, 0,25% 0,50%, 0,75%, 1,00% e 10% em massa de fotoiniciador foram adicionadas em uma matriz polimérica composta por TEGDMA/BisGMA 50%/50% em massa de forma que, fixando variáveis externas referentes à fonte de luz e à preparação das amostras, foi possível avaliar o efeito da concentração de fotoiniciador nas propriedades mecânicas de resistência à fratura por compressão, resistência à fratura pela aplicação de tensão diametral e dureza Barcol. Por fim, o efeito da concentração na cor aferida através do método CIELab foi investigada. Os fotoiniciadores utilizados foram o Irgacure® 819, a 1-fenil-1,2-propanodiona (PPD) e a Canforoquinona a qual foi utilizada juntamente com ocoiniciador Etil-4 dimetilaminobenzoato (EDB) na concentração constante de 1% em massa. Os resultados mecânicos e de cor foram comparados entre as diferentes amostras através de análises estatísticas (ANOVA) e, especificamente para cor, o parâmetro de diferença de cor (ΔE) foi interpretado verificar se as alterações observadas são perceptíveis ao olho humano. Para fundamentar os estudos, análises do espectro de absorção das amostras, do espectro de irradiação da fonte de luz e do grau de conversão das amostras foram realizadas. Os resultados revelaram que, independentemente do fotoiniciador, graus de conversão da mesma ordem de grandeza de um adesivo comercial foram obtidos, porém as velocidades de reação foram diferentes (maior velocidade para as amostras de CQ e menor para PPD). Curvas características foram obtidas para os espectros de absorção e de irradiação confirmando, pela sobreposição das curvas, que a fonte de luz é efetiva para iniciação da polimerização das amostras. As análises de resistência à fratura revelaram que a quebra catastrófica do material ocorrerá preferencialmente quando a força é aplicada ao longo do diâmetro para os corpos de prova preparados. Quanto à dureza, verificou-se que que para a CQ houve um máximo, para Irgacure um comportamento assintótico com aumento da concentração e, para a PPD, não foi possível a obtenção de amostras (verificado que a PPD necessita de tempo de irradiação superior ao convencionalmente utilizado na prática odontológica). Os testes de ANOVA permitiram verificar que o Irgacure é capaz de fornecer resultados mecânicos semelhante em relação à CQ ocasionando, em contrapartida, um menor escurecimento e amarelamento. Analisando o parâmetro ΔE, confirmou-se que a alteração na cor se torna evidente à medida que ocorre o aumento da concentração de fotoiniciador independentemente do fotoiniciador utilizado, porém a alteração é maior para a CQ.

Projection-based atom selection in orthogonal matching pursuit for compressive sensing

For compressive sensing, we endeavor to improve the atom selection strategy of the existing orthogonal matching pursuit (OMP) algorithm. To achieve a better estimate of the underlying support set progressively through iterations, we use a least squares solution based atom selection method. From a set of promising atoms, the choice of an atom is performed through a new method that uses orthogonal projection along-with a standard matched filter. Through experimental evaluations, the effect of projection based atom selection strategy is shown to provide a significant improvement for the support set recovery performance, in turn, the compressive sensing recovery.

Imaging through turbulence using compressive coherence sensing.

Previous studies have shown that the isoplanatic distortion due to turbulence and the image of a remote object may be jointly estimated from the 4D mutual intensity across an aperture. This Letter shows that decompressive inference on a 2D slice of the 4D mutual intensity, as measured by a rotational shear interferometer, is sufficient for estimation of sparse objects imaged through turbulence. The 2D slice is processed using an iterative algorithm that alternates between estimating the sparse objects and estimating the turbulence-induced phase screen. This approach may enable new systems that infer object properties through turbulence without exhaustive sampling of coherence functions.

Task-driven adaptive statistical compressive sensing of gaussian mixture models

A framework for adaptive and non-adaptive statistical compressive sensing is developed, where a statistical model replaces the standard sparsity model of classical compressive sensing. We propose within this framework optimal task-specific sensing protocols specifically and jointly designed for classification and reconstruction. A two-step adaptive sensing paradigm is developed, where online sensing is applied to detect the signal class in the first step, followed by a reconstruction step adapted to the detected class and the observed samples. The approach is based on information theory, here tailored for Gaussian mixture models (GMMs), where an information-theoretic objective relationship between the sensed signals and a representation of the specific task of interest is maximized. Experimental results using synthetic signals, Landsat satellite attributes, and natural images of different sizes and with different noise levels show the improvements achieved using the proposed framework when compared to more standard sensing protocols. The underlying formulation can be applied beyond GMMs, at the price of higher mathematical and computational complexity. © 1991-2012 IEEE.