On uncertainty propagation in image-guided renal navigation: Exploring uncertainty reduction techniques through simulation and in vitro phantom evaluation

Image-guided interventions (IGIs) entail the use of imaging to augment or replace direct vision during therapeutic interventions, with the overall goal is to provide effective treatment in a less invasive manner, as an alternative to traditional open surgery, while reducing patient trauma and shortening the recovery time post-procedure. IGIs rely on pre-operative images, surgical tracking and localization systems, and intra-operative images to provide correct views of the surgical scene. Pre-operative images are used to generate patient-specific anatomical models that are then registered to the patient using the surgical tracking system, and often complemented with real-time, intra-operative images. IGI systems are subject to uncertainty from several sources, including surgical instrument tracking / localization uncertainty, model-to-patient registration uncertainty, user-induced navigation uncertainty, as well as the uncertainty associated with the calibration of various surgical instruments and intra-operative imaging devices (i.e., laparoscopic camera) instrumented with surgical tracking sensors. All these uncertainties impact the overall targeting accuracy, which represents the error associated with the navigation of a surgical instrument to a specific target to be treated under image guidance provided by the IGI system. Therefore, understanding the overall uncertainty of an IGI system is paramount to the overall outcome of the intervention, as procedure success entails achieving certain accuracy tolerances specific to individual procedures. This work has focused on studying the navigation uncertainty, along with techniques to reduce uncertainty, for an IGI platform dedicated to image-guided renal interventions. We constructed life-size replica patient-specific kidney models from pre-operative images using 3D printing and tissue emulating materials and conducted experiments to characterize the uncertainty of both optical and electromagnetic surgical tracking systems, the uncertainty associated with the virtual model-to-physical phantom registration, as well as the uncertainty associated with live augmented reality (AR) views of the surgical scene achieved by enhancing the pre-procedural model and tracked surgical instrument views with live video views acquires using a camera tracked in real time. To better understand the effects of the tracked instrument calibration, registration fiducial configuration, and tracked camera calibration on the overall navigation uncertainty, we conducted Monte Carlo simulations that enabled us to identify optimal configurations that were subsequently validated experimentally using patient-specific phantoms in the laboratory. To mitigate the inherent accuracy limitations associated with the pre-procedural model-to-patient registration and their effect on the overall navigation, we also demonstrated the use of tracked video imaging to update the registration, enabling us to restore targeting accuracy to within its acceptable range. Lastly, we conducted several validation experiments using patient-specific kidney emulating phantoms using post-procedure CT imaging as reference ground truth to assess the accuracy of AR-guided navigation in the context of in vitro renal interventions. This work helped find answers to key questions about uncertainty propagation in image-guided renal interventions and led to the development of key techniques and tools to help reduce optimize the overall navigation / targeting uncertainty

MRI Artefact Augmentation: Robust Deep Learning Systems and Automated Quality Control

Quality control (QC) of magnetic resonance imaging (MRI) is essential to establish whether a scan or dataset meets a required set of standards. In MRI, many potential artefacts must be identified so that problematic images can either be excluded or accounted for in further image processing or analysis. To date, the gold standard for the identification of these issues is visual inspection by experts. A primary source of MRI artefacts is caused by patient movement, which can affect clinical diagnosis and impact the accuracy of Deep Learning systems. In this thesis, I present a method to simulate motion artefacts from artefact-free images to augment convolutional neural networks (CNNs), increasing training appearance variability and robustness to motion artefacts. I show that models trained with artefact augmentation generalise better and are more robust to real-world artefacts, with negligible cost to performance on clean data. I argue that it is often better to optimise frameworks end-to-end with artefact augmentation rather than learning to retrospectively remove artefacts, thus enforcing robustness to artefacts at the feature level representation of the data. The labour-intensive and subjective nature of QC has increased interest in automated methods. To address this, I approach MRI quality estimation as the uncertainty in performing a downstream task, using probabilistic CNNs to predict segmentation uncertainty as a function of the input data. Extending this framework, I introduce a novel decoupled uncertainty model, enabling separate uncertainty predictions for different types of image degradation. Training with an extended k-space artefact augmentation pipeline, the model provides informative measures of uncertainty on problematic real-world scans classified by QC raters and enables sources of segmentation uncertainty to be identified. Suitable quality for algorithmic processing may differ from an image's perceptual quality. Exploring this, I pose MRI visual quality assessment as an image restoration task. Using Bayesian CNNs to recover clean images from noisy data, I show that the uncertainty indicates the possible recoverability of an image. A multi-task network combining uncertainty-aware artefact recovery with tissue segmentation highlights the distinction between visual and algorithmic quality, which has the impact that, depending on the downstream task, less data should be discarded for purely visual quality reasons

Augmented Reality Ultrasound Guidance in Anesthesiology

Real-time ultrasound has become a mainstay in many image-guided interventions and increasingly popular in several percutaneous procedures in anesthesiology. One of the main constraints of ultrasound-guided needle interventions is identifying and distinguishing the needle tip from needle shaft in the image. Augmented reality (AR) environments have been employed to address challenges surrounding surgical tool visualization, navigation, and positioning in many image-guided interventions. The motivation behind this work was to explore the feasibility and utility of such visualization techniques in anesthesiology to address some of the specific limitations of ultrasound-guided needle interventions. This thesis brings together the goals, guidelines, and best development practices of functional AR ultrasound image guidance (AR-UIG) systems, examines the general structure of such systems suitable for applications in anesthesiology, and provides a series of recommendations for their development. The main components of such systems, including ultrasound calibration and system interface design, as well as applications of AR-UIG systems for quantitative skill assessment, were also examined in this thesis. The effects of ultrasound image reconstruction techniques, as well as phantom material and geometry on ultrasound calibration, were investigated. Ultrasound calibration error was reduced by 10% with synthetic transmit aperture imaging compared with B-mode ultrasound. Phantom properties were shown to have a significant effect on calibration error, which is a variable based on ultrasound beamforming techniques. This finding has the potential to alter how calibration phantoms are designed cognizant of the ultrasound imaging technique. Performance of an AR-UIG guidance system tailored to central line insertions was evaluated in novice and expert user studies. While the system outperformed ultrasound-only guidance with novice users, it did not significantly affect the performance of experienced operators. Although the extensive experience of the users with ultrasound may have affected the results, certain aspects of the AR-UIG system contributed to the lackluster outcomes, which were analyzed via a thorough critique of the design decisions. The application of an AR-UIG system in quantitative skill assessment was investigated, and the first quantitative analysis of needle tip localization error in ultrasound in a simulated central line procedure, performed by experienced operators, is presented. Most participants did not closely follow the needle tip in ultrasound, resulting in 42% unsuccessful needle placements and a 33% complication rate. Compared to successful trials, unsuccessful procedures featured a significantly greater (p=0.04) needle-tip to image-plane distance. Professional experience with ultrasound does not necessarily lead to expert level performance. Along with deliberate practice, quantitative skill assessment may reinforce clinical best practices in ultrasound-guided needle insertions. Based on the development guidelines, an AR-UIG system was developed to address the challenges in ultrasound-guided epidural injections. For improved needle positioning, this system integrated A-mode ultrasound signal obtained from a transducer housed at the tip of the needle. Improved needle navigation was achieved via enhanced visualization of the needle in an AR environment, in which B-mode and A-mode ultrasound data were incorporated. The technical feasibility of the AR-UIG system was evaluated in a preliminary user study. The results suggested that the AR-UIG system has the potential to outperform ultrasound-only guidance

Medical Image Registration: Statistical Models of Performance in Relation to the Statistical Characteristics of the Image Data

For image-guided interventions, the imaging task often pertains to registering preoperative and intraoperative images within a common coordinate system. While the accuracy of the registration is directly tied to the accuracy of targeting in the intervention (and presumably the success of the medical outcome), there is relatively little quantitative understanding of the fundamental factors that govern image registration accuracy. A statistical framework is presented that relates models of image noise and spatial resolution to the task of registration, giving theoretical limits on registration accuracy and providing guidance for the selection of image acquisition and post-processing parameters. The framework is further shown to model the confounding influence of soft-tissue deformation in rigid image registration — accurately predicting the reduction in registration accuracy and revealing similarity metrics that are robust against such effects. Furthermore, the framework is shown to provide conceptual guidance in the development of a novel CT-to-radiograph registration method that accounts for deformation. The work also examines a learning-based method for deformable registration to investigate how the statistical characteristics of the training data affect the ability of the model to generalize to test data with differing statistical characteristics. The analysis provides insight on the benefits of statistically diverse training data in generalizability of a neural network and is further applied to the development of a learning-based MR-to-CT synthesis method. Overall, the work yields a quantitative approach to theoretically and experimentally relate the accuracy of image registration to the statistical characteristics of the image data, providing a rigorous guide to the development of new registration methods

Neuromagnetic Decomposition of Social Interaction

Not Available

Accurate Targeting of Liver Tumors in Stereotactic Radiation Therapy

This doctoral thesis concerns the treatment of liver cancer patients using external beam radiotherapy. The quality of this treatment greatly depends on delivering a high radiation dose to the tumor while keeping the dose as low as possible to surrounding healthy tissues. One of the major challenges is locating the tumor at the moment of dose delivery. In this ork, the uncertainty of locating the tumor was investigated. For this purpose, gold markers were implanted in the liver tissue and visualized on X-ray images. The markers were used to measure day-to-day tumor mobility and motion due to respiration. Furthermore, it was found that major improvements in the targeting accuracy can be achieved by using the markers for guiding the treatment procedure

Adaptive Vision Based Scene Registration for Outdoor Augmented Reality

Augmented Reality (AR) involves adding virtual content into real scenes. Scenes are viewed using a Head-Mounted Display or other display type. In order to place content into the user's view of a scene, the user's position and orientation relative to the scene, commonly referred to as their pose, must be determined accurately. This allows the objects to be placed in the correct positions and to remain there when the user moves or the scene changes. It is achieved by tracking the user in relation to their environment using a variety of technology. One technology which has proven to provide accurate results is computer vision. Computer vision involves a computer analysing images and achieving an understanding of them. This may be locating objects such as faces in the images, or in the case of AR, determining the pose of the user. One of the ultimate goals of AR systems is to be capable of operating under any condition. For example, a computer vision system must be robust under a range of different scene types, and under unpredictable environmental conditions due to variable illumination and weather. The majority of existing literature tests algorithms under the assumption of ideal or 'normal' imaging conditions. To ensure robustness under as many circumstances as possible it is also important to evaluate the systems under adverse conditions. This thesis seeks to analyse the effects that variable illumination has on computer vision algorithms. To enable this analysis, test data is required to isolate weather and illumination effects, without other factors such as changes in viewpoint that would bias the results. A new dataset is presented which also allows controlled viewpoint differences in the presence of weather and illumination changes. This is achieved by capturing video from a camera undergoing a repeatable motion sequence. Ground truth data is stored per frame allowing images from the same position under differing environmental conditions, to be easily extracted from the videos. An in depth analysis of six detection algorithms and five matching techniques demonstrates the impact that non-uniform illumination changes can have on vision algorithms. Specifically, shadows can degrade performance and reduce confidence in the system, decrease reliability, or even completely prevent successful operation. An investigation into approaches to improve performance yields techniques that can help reduce the impact of shadows. A novel algorithm is presented that merges reference data captured at different times, resulting in reference data with minimal shadow effects. This can significantly improve performance and reliability when operating on images containing shadow effects. These advances improve the robustness of computer vision systems and extend the range of conditions in which they can operate. This can increase the usefulness of the algorithms and the AR systems that employ them

EVALUATION OF ARTIFACTS IN EXPERIMENTAL CINE 4D CT ACQUISITION METHODS

Four-dimensional computed tomography (4D CT) has increased the accuracy of radiation treatment planning for patients in whom the extent of target motion is large. 4D CT has become a standard of care for radiation treatment simulation, allowing decreased motion artifacts and increased spatiotemporal localization of anatomical structures that move. However, motion artifacts may still remain. These artifacts, or artificial anatomic spatial distributions, add a systematic uncertainty to the treatment process and limit the accuracy of lung function images derived from CT. We proposed to reduce the motion artifacts in cine 4D CT by using three novel investigational 4D CT acquisition methods: (1) oversampling the data acquired, (2) gating the x-ray beam with breathing irregularities, and (3) rescanning areas of the clinical standard 4D CT associated with high breathing irregularities. These experimental acquisitions were tested through a protocol approved by the institutional review board with 18 patients with a primary thoracic malignancy receiving a standard 4D CT scan for radiation treatment simulation. The artifact presence in all 4D CT scans was assessed by an automated artifact quantification metric. This artifact metric was validated by a rigorous receiver operating characteristic (ROC) analysis using a high-quality dataset derived from a group of expert observers who reached a consensus decision on the artifact frequency and magnitude for each of 10 clinical 4D CT scans from patients with primary thoracic cancer. The clinical and experimental 4D CT acquisitions from the 18 patients on the protocol were post-processed by the clinical standard of phase sorting and by an experimental phase sorting that incorporated the validated artifact metric. The 4D CT acquisition and processing method judged to be the most improved was the oversampling acquisition with the experimental sorting. The reproducibility of this improved method was tested on a second distinct cohort of 10 patients with a primary thoracic malignancy. Those patients received a clinical phase-sorted 4D CT immediately followed by three independent oversampling acquisitions, processed by the experimental sorting method and evaluated using the artifact metric. The experimental-sorted oversampling acquisition produced a statistically significant artifact reduction (27% and 28% per cohort) from the phase-sorted clinical standard acquisition