Toward quantitative limited-angle ultrasound reflection tomography to inform abdominal HIFU treatment planning

High-Intensity Focused Ultrasound (HIFU) is a treatment modality for solid cancers of the liver and pancreas which is non-invasive and free from many of the side-effects of radiotherapy and chemotherapy. The safety and efficacy of abdominal HIFU treatment is dependent on the ability to bring the therapeutic sound waves to a small focal ”lesion” of known and controllable location within the patient anatomy. To achieve this, pre-treatment planning typically includes a numerical simulation of the therapeutic ultrasound beam, in which anatomical compartment locations are derived from computed tomography or magnetic resonance images. In such planning simulations, acoustic properties such as density and speed-of-sound are assumed for the relevant tissues which are rarely, if ever, determined specifically for the patient. These properties are known to vary between patients and disease states of tissues, and to influence the intensity and location of the HIFU lesion. The subject of this thesis is the problem of non-invasive patient-specific measurement of acoustic tissue properties. The appropriate method, also, of establishing spatial correspondence between physical ultrasound transducers and modeled (imaged) anatomy via multimodal image reg-istration is also investigated; this is of relevance both to acoustic tissue property estimation and to the guidance of HIFU delivery itself. First, the principle of a method is demonstrated with which acoustic properties can be recovered for several tissues simultaneously using reflection ultrasound, given accurate knowledge of the physical locations of tissue compartments. Second, the method is developed to allow for some inaccuracy in this knowledge commensurate with the inaccuracy typical in abdominal multimodal image registration. Third, several current multimodal image registration techniques, and two novel modifications, are compared for accuracy and robustness. In conclusion, relevant acoustic tissue properties can, in principle, be estimated using reflected ultrasound data that could be acquired using diagnostic imaging transducers in a clinical setting

Foetal echocardiographic segmentation

Congenital heart disease affects just under one percentage of all live births [1]. Those defects that manifest themselves as changes to the cardiac chamber volumes are the motivation for the research presented in this thesis. Blood volume measurements in vivo require delineation of the cardiac chambers and manual tracing of foetal cardiac chambers is very time consuming and operator dependent. This thesis presents a multi region based level set snake deformable model applied in both 2D and 3D which can automatically adapt to some extent towards ultrasound noise such as attenuation, speckle and partial occlusion artefacts. The algorithm presented is named Mumford Shah Sarti Collision Detection (MSSCD). The level set methods presented in this thesis have an optional shape prior term for constraining the segmentation by a template registered to the image in the presence of shadowing and heavy noise. When applied to real data in the absence of the template the MSSCD algorithm is initialised from seed primitives placed at the centre of each cardiac chamber. The voxel statistics inside the chamber is determined before evolution. The MSSCD stops at open boundaries between two chambers as the two approaching level set fronts meet. This has significance when determining volumes for all cardiac compartments since cardiac indices assume that each chamber is treated in isolation. Comparison of the segmentation results from the implemented snakes including a previous level set method in the foetal cardiac literature show that in both 2D and 3D on both real and synthetic data, the MSSCD formulation is better suited to these types of data. All the algorithms tested in this thesis are within 2mm error to manually traced segmentation of the foetal cardiac datasets. This corresponds to less than 10% of the length of a foetal heart. In addition to comparison with manual tracings all the amorphous deformable model segmentations in this thesis are validated using a physical phantom. The volume estimation of the phantom by the MSSCD segmentation is to within 13% of the physically determined volume

Ultrasound Signal Processing: From Models to Deep Learning

Medical ultrasound imaging relies heavily on high-quality signal processing algorithms to provide reliable and interpretable image reconstructions. Hand-crafted reconstruction methods, often based on approximations of the underlying measurement model, are useful in practice, but notoriously fall behind in terms of image quality. More sophisticated solutions, based on statistical modelling, careful parameter tuning, or through increased model complexity, can be sensitive to different environments. Recently, deep learning based methods have gained popularity, which are optimized in a data-driven fashion. These model-agnostic methods often rely on generic model structures, and require vast training data to converge to a robust solution. A relatively new paradigm combines the power of the two: leveraging data-driven deep learning, as well as exploiting domain knowledge. These model-based solutions yield high robustness, and require less trainable parameters and training data than conventional neural networks. In this work we provide an overview of these methods from the recent literature, and discuss a wide variety of ultrasound applications. We aim to inspire the reader to further research in this area, and to address the opportunities within the field of ultrasound signal processing. We conclude with a future perspective on these model-based deep learning techniques for medical ultrasound applications

Hierarchical template matching for 3D myocardial tracking and cardiac strain estimation

Myocardial tracking and strain estimation can non-invasively assess cardiac functioning using subject-specific MRI. As the left-ventricle does not have a uniform shape and functioning from base to apex, the development of 3D MRI has provided opportunities for simultaneous 3D tracking, and 3D strain estimation. We have extended a Local Weighted Mean (LWM) transformation function for 3D, and incorporated in a Hierarchical Template Matching model to solve 3D myocardial tracking and strain estimation problem. The LWM does not need to solve a large system of equations, provides smooth displacement of myocardial points, and adapt local geometric differences in images. Hence, 3D myocardial tracking can be performed with 1.49 mm median error, and without large error outliers. The maximum error of tracking is up to 24% reduced compared to benchmark methods. Moreover, the estimated strain can be insightful to improve 3D imaging protocols, and the computer code of LWM could also be useful for geo-spatial and manufacturing image analysis researchers

Patient-specific simulation environment for surgical planning and preoperative rehearsal

Surgical simulation is common practice in the fields of surgical education and training. Numerous surgical simulators are available from commercial and academic organisations for the generic modelling of surgical tasks. However, a simulation platform is still yet to be found that fulfils the key requirements expected for patient-specific surgical simulation of soft tissue, with an effective translation into clinical practice. Patient-specific modelling is possible, but to date has been time-consuming, and consequently costly, because data preparation can be technically demanding. This motivated the research developed herein, which addresses the main challenges of biomechanical modelling for patient-specific surgical simulation. A novel implementation of soft tissue deformation and estimation of the patient-specific intraoperative environment is achieved using a position-based dynamics approach. This modelling approach overcomes the limitations derived from traditional physically-based approaches, by providing a simulation for patient-specific models with visual and physical accuracy, stability and real-time interaction. As a geometrically- based method, a calibration of the simulation parameters is performed and the simulation framework is successfully validated through experimental studies. The capabilities of the simulation platform are demonstrated by the integration of different surgical planning applications that are found relevant in the context of kidney cancer surgery. The simulation of pneumoperitoneum facilitates trocar placement planning and intraoperative surgical navigation. The implementation of deformable ultrasound simulation can assist surgeons in improving their scanning technique and definition of an optimal procedural strategy. Furthermore, the simulation framework has the potential to support the development and assessment of hypotheses that cannot be tested in vivo. Specifically, the evaluation of feedback modalities, as a response to user-model interaction, demonstrates improved performance and justifies the need to integrate a feedback framework in the robot-assisted surgical setting.Open Acces

Left-ventricular epi- and endocardium extraction from 3D ultrasound images using an automatically constructed 3D ASM

© 2014 Taylor & Francis.In this paper, we propose an automatic method for constructing an active shape model (ASM) to segment the complete cardiac left ventricle in 3D ultrasound (3DUS) images, which avoids costly manual landmarking. The automatic construction of the ASM has already been addressed in the literature; however, the direct application of these methods to 3DUS is hampered by a high level of noise and artefacts. Therefore, we propose to construct the ASM by fusing the multidetector computed tomography data, to learn the shape, with the artificially generated 3DUS, in order to learn the neighbourhood of the boundaries. Our artificial images were generated by two approaches: a faster one that does not take into account the geometry of the transducer, and a more comprehensive one, implemented in Field II toolbox. The segmentation accuracy of our ASM was evaluated on 20 patients with left-ventricular asynchrony, demonstrating plausibility of the approach