Hierarchical alignment of breast DCE-MR images by groupwise registration and robust feature matching: Breast DCE-MR image registration

Purpose: Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) shows high sensitivity in detecting breast cancer. However, its performance could be affected by patient motion during the imaging. To overcome this problem, it is necessary to correct patient motion by deformable registration, before using the DCE-MRI to detect breast cancer. However, deformable registration of DCE-MR images is challenging due to the dramatic contrast change over time (especially between the precontrast and postcontrast images). Most existing methods typically register each postcontrast image onto the precontrast image independently, without considering the dynamic contrast change after agent uptake. This could lead to the inconsistency among the aligned postcontrast images in the precontrast image space, which will eventually result in worse performance in cancer detection. In this paper, the authors present a novel hierarchical registration framework to address this problem

Respiratory motion correction in dynamic MRI using robust data decomposition registration - Application to DCE-MRI.

Motion correction in Dynamic Contrast Enhanced (DCE-) MRI is challenging because rapid intensity changes can compromise common (intensity based) registration algorithms. In this study we introduce a novel registration technique based on robust principal component analysis (RPCA) to decompose a given time-series into a low rank and a sparse component. This allows robust separation of motion components that can be registered, from intensity variations that are left unchanged. This Robust Data Decomposition Registration (RDDR) is demonstrated on both simulated and a wide range of clinical data. Robustness to different types of motion and breathing choices during acquisition is demonstrated for a variety of imaged organs including liver, small bowel and prostate. The analysis of clinically relevant regions of interest showed both a decrease of error (15-62% reduction following registration) in tissue time-intensity curves and improved areas under the curve (AUC60) at early enhancement

Analysis of contrast-enhanced medical images.

Early detection of human organ diseases is of great importance for the accurate diagnosis and institution of appropriate therapies. This can potentially prevent progression to end-stage disease by detecting precursors that evaluate organ functionality. In addition, it also assists the clinicians for therapy evaluation, tracking diseases progression, and surgery operations. Advances in functional and contrast-enhanced (CE) medical images enabled accurate noninvasive evaluation of organ functionality due to their ability to provide superior anatomical and functional information about the tissue-of-interest. The main objective of this dissertation is to develop a computer-aided diagnostic (CAD) system for analyzing complex data from CE magnetic resonance imaging (MRI). The developed CAD system has been tested in three case studies: (i) early detection of acute renal transplant rejection, (ii) evaluation of myocardial perfusion in patients with ischemic heart disease after heart attack; and (iii), early detection of prostate cancer. However, developing a noninvasive CAD system for the analysis of CE medical images is subject to multiple challenges, including, but are not limited to, image noise and inhomogeneity, nonlinear signal intensity changes of the images over the time course of data acquisition, appearances and shape changes (deformations) of the organ-of-interest during data acquisition, determination of the best features (indexes) that describe the perfusion of a contrast agent (CA) into the tissue. To address these challenges, this dissertation focuses on building new mathematical models and learning techniques that facilitate accurate analysis of CAs perfusion in living organs and include: (i) accurate mathematical models for the segmentation of the object-of-interest, which integrate object shape and appearance features in terms of pixel/voxel-wise image intensities and their spatial interactions; (ii) motion correction techniques that combine both global and local models, which exploit geometric features, rather than image intensities to avoid problems associated with nonlinear intensity variations of the CE images; (iii) fusion of multiple features using the genetic algorithm. The proposed techniques have been integrated into CAD systems that have been tested in, but not limited to, three clinical studies. First, a noninvasive CAD system is proposed for the early and accurate diagnosis of acute renal transplant rejection using dynamic contrast-enhanced MRI (DCE-MRI). Acute rejection–the immunological response of the human immune system to a foreign kidney–is the most sever cause of renal dysfunction among other diagnostic possibilities, including acute tubular necrosis and immune drug toxicity. In the U.S., approximately 17,736 renal transplants are performed annually, and given the limited number of donors, transplanted kidney salvage is an important medical concern. Thus far, biopsy remains the gold standard for the assessment of renal transplant dysfunction, but only as the last resort because of its invasive nature, high cost, and potential morbidity rates. The diagnostic results of the proposed CAD system, based on the analysis of 50 independent in-vivo cases were 96% with a 95% confidence interval. These results clearly demonstrate the promise of the proposed image-based diagnostic CAD system as a supplement to the current technologies, such as nuclear imaging and ultrasonography, to determine the type of kidney dysfunction. Second, a comprehensive CAD system is developed for the characterization of myocardial perfusion and clinical status in heart failure and novel myoregeneration therapy using cardiac first-pass MRI (FP-MRI). Heart failure is considered the most important cause of morbidity and mortality in cardiovascular disease, which affects approximately 6 million U.S. patients annually. Ischemic heart disease is considered the most common underlying cause of heart failure. Therefore, the detection of the heart failure in its earliest forms is essential to prevent its relentless progression to premature death. While current medical studies focus on detecting pathological tissue and assessing contractile function of the diseased heart, this dissertation address the key issue of the effects of the myoregeneration therapy on the associated blood nutrient supply. Quantitative and qualitative assessment in a cohort of 24 perfusion data sets demonstrated the ability of the proposed framework to reveal regional perfusion improvements with therapy, and transmural perfusion differences across the myocardial wall; thus, it can aid in follow-up on treatment for patients undergoing the myoregeneration therapy. Finally, an image-based CAD system for early detection of prostate cancer using DCE-MRI is introduced. Prostate cancer is the most frequently diagnosed malignancy among men and remains the second leading cause of cancer-related death in the USA with more than 238,000 new cases and a mortality rate of about 30,000 in 2013. Therefore, early diagnosis of prostate cancer can improve the effectiveness of treatment and increase the patient’s chance of survival. Currently, needle biopsy is the gold standard for the diagnosis of prostate cancer. However, it is an invasive procedure with high costs and potential morbidity rates. Additionally, it has a higher possibility of producing false positive diagnosis due to relatively small needle biopsy samples. Application of the proposed CAD yield promising results in a cohort of 30 patients that would, in the near future, represent a supplement of the current technologies to determine prostate cancer type. The developed techniques have been compared to the state-of-the-art methods and demonstrated higher accuracy as shown in this dissertation. The proposed models (higher-order spatial interaction models, shape models, motion correction models, and perfusion analysis models) can be used in many of today’s CAD applications for early detection of a variety of diseases and medical conditions, and are expected to notably amplify the accuracy of CAD decisions based on the automated analysis of CE images

Improving Accuracy of Information Extraction from Quantitative Magnetic Resonance Imaging

Quantitative MRI offers the possibility to produce objective measurements of tissue physiology at different scales. Such measurements are highly valuable in applications such as drug development, treatment monitoring or early diagnosis of cancer. From microstructural information in diffusion weighted imaging (DWI) or local perfusion and permeability in dynamic contrast (DCE-) MRI to more macroscopic observations of the local intestinal contraction, a number of aspects of quantitative MRI are considered in this thesis. The main objective of the presented work is to provide pre-processing techniques and model modification in order to improve the reliability of image analysis in quantitative MRI. Firstly, the challenge of clinical DWI signal modelling is investigated to overcome the biasing effect due to noise in the data. Several methods with increasing level of complexity are applied to simulations and a series of clinical datasets. Secondly, a novel Robust Data Decomposition Registration technique is introduced to tackle the problem of image registration in DCE-MRI. The technique allows the separation of tissue enhancement from motion effects so that the latter can be corrected independently. It is successfully applied to DCE-MRI datasets of different organs. This application is extended to the correction of respiratory motion in small bowel motility quantification in dynamic MRI data acquired during free breathing. Finally, a new local model for the arterial input function (AIF) is proposed. The estimation of the arterial blood contrast agent concentration in DCE-MRI is augmented using prior knowledge on local tissue structure from DWI. This work explores several types of imaging using MRI. It contributes to clinical quantitative MRI analysis providing practical solutions aimed at improving the accuracy and consistency of the parameters derived from image data

Advanced Medical Image Registration Methods for Quantitative Imaging and Multi-Channel Images

This thesis proposes advanced medical image registration methods for applications that can be grouped in two broad themes. The first theme focuses on registration techniques increasing the reliability of _quantitative measurements_ extracted from sets of medical images. The second theme that is considered in this thesis is the registration of _multi-channel_ images

Pattern classification approaches for breast cancer identification via MRI: state‐of‐the‐art and vision for the future

Mining algorithms for Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCEMRI) of breast tissue are discussed. The algorithms are based on recent advances in multidimensional signal processing and aim to advance current state‐of‐the‐art computer‐aided detection and analysis of breast tumours when these are observed at various states of development. The topics discussed include image feature extraction, information fusion using radiomics, multi‐parametric computer‐aided classification and diagnosis using information fusion of tensorial datasets as well as Clifford algebra based classification approaches and convolutional neural network deep learning methodologies. The discussion also extends to semi‐supervised deep learning and self‐supervised strategies as well as generative adversarial networks and algorithms using generated confrontational learning approaches. In order to address the problem of weakly labelled tumour images, generative adversarial deep learning strategies are considered for the classification of different tumour types. The proposed data fusion approaches provide a novel Artificial Intelligence (AI) based framework for more robust image registration that can potentially advance the early identification of heterogeneous tumour types, even when the associated imaged organs are registered as separate entities embedded in more complex geometric spaces. Finally, the general structure of a high‐dimensional medical imaging analysis platform that is based on multi‐task detection and learning is proposed as a way forward. The proposed algorithm makes use of novel loss functions that form the building blocks for a generated confrontation learning methodology that can be used for tensorial DCE‐MRI. Since some of the approaches discussed are also based on time‐lapse imaging, conclusions on the rate of proliferation of the disease can be made possible. The proposed framework can potentially reduce the costs associated with the interpretation of medical images by providing automated, faster and more consistent diagnosis

Model-driven registration for multi-parametric renal MRI

The use of MR imaging biomarkers is a promising technique that may assist towards faster prognosis and more accurate diagnosis of diseases like diabetic kidney disease (DKD). The quantification of MR Imaging renal biomarkers from multiparametric MRI is a process that requires a physiological model to be fitted on the data. This process can provide accurate estimates only under the assumption that there is pixelto-pixel correspondence between images acquired over different time points. However, this is rarely the case due to motion artifacts (breathing, involuntary muscle relaxation) introduced during the acquisition. Hence, it is of vital importance for a biomarkers quantification pipeline to include a motion correctionstep in order to properly align the images and enable a more accurate parameter estimation. This study aims in testing whether a Model Driven Registration (MDR), which integrates physiological models in the registration process itself, can serve as a universal solution for the registration of multiparametric renal MRI. MDR is compared with a state-of-the-art model-free motion correction approach for multiparametric MRI, that minimizes a Principal Components Analysis based metric, performing a groupwise registration. The results of the two methods are compared on T1, DTI and DCE-MRI data for a small cohort of 10 DKD patients, obtained from BEAt-DKD project’s digital database. The majority of the evaluation metrics used to compare the two methods indicated that MDR achieved better registration results, while requiring significantly lower computational times. In conclusion, MDR could be considered as the method of choice for motion correction of multiparametric quantitative renal MRI