A Deep Learning Framework for Unsupervised Affine and Deformable Image Registration

Image registration, the process of aligning two or more images, is the core technique of many (semi-)automatic medical image analysis tasks. Recent studies have shown that deep learning methods, notably convolutional neural networks (ConvNets), can be used for image registration. Thus far training of ConvNets for registration was supervised using predefined example registrations. However, obtaining example registrations is not trivial. To circumvent the need for predefined examples, and thereby to increase convenience of training ConvNets for image registration, we propose the Deep Learning Image Registration (DLIR) framework for \textit{unsupervised} affine and deformable image registration. In the DLIR framework ConvNets are trained for image registration by exploiting image similarity analogous to conventional intensity-based image registration. After a ConvNet has been trained with the DLIR framework, it can be used to register pairs of unseen images in one shot. We propose flexible ConvNets designs for affine image registration and for deformable image registration. By stacking multiple of these ConvNets into a larger architecture, we are able to perform coarse-to-fine image registration. We show for registration of cardiac cine MRI and registration of chest CT that performance of the DLIR framework is comparable to conventional image registration while being several orders of magnitude faster.Comment: Accepted: Medical Image Analysis - Elsevie

Improvements in the registration of multimodal medical imaging : application to intensity inhomogeneity and partial volume corrections

Alignment or registration of medical images has a relevant role on clinical diagnostic and treatment decisions as well as in research settings. With the advent of new technologies for multimodal imaging, robust registration of functional and anatomical information is still a challenge, particular in small-animal imaging given the lesser structural content of certain anatomical parts, such as the brain, than in humans. Besides, patient-dependent and acquisition artefacts affecting the images information content further complicate registration, as is the case of intensity inhomogeneities (IIH) showing in MRI and the partial volume effect (PVE) attached to PET imaging. Reference methods exist for accurate image registration but their performance is severely deteriorated in situations involving little images Overlap. While several approaches to IIH and PVE correction exist these methods still do not guarantee or rely on robust registration. This Thesis focuses on overcoming current limitations af registration to enable novel IIH and PVE correction methods.El registre d'imatges mèdiques té un paper rellevant en les decisions de diagnòstic i tractament clíniques així com en la recerca. Amb el desenvolupament de noves tecnologies d'imatge multimodal, el registre robust d'informació funcional i anatòmica és encara avui un repte, en particular, en imatge de petit animal amb un menor contingut estructural que en humans de certes parts anatòmiques com el cervell. A més, els artefactes induïts pel propi pacient i per la tècnica d'adquisició que afecten el contingut d'informació de les imatges complica encara més el procés de registre. És el cas de les inhomogeneïtats d'intensitat (IIH) que apareixen a les RM i de l'efecte de volum parcial (PVE) característic en PET. Tot i que existeixen mètodes de referència pel registre acurat d'imatges la seva eficàcia es veu greument minvada en casos de poc solapament entre les imatges. De la mateixa manera, també existeixen mètodes per la correcció d'IIH i de PVE però que no garanteixen o que requereixen un registre robust. Aquesta tesi es centra en superar aquestes limitacions sobre el registre per habilitar nous mètodes per la correcció d'IIH i de PVE

Dynamic Image Processing for Guidance of Off-pump Beating Heart Mitral Valve Repair

Compared to conventional open heart procedures, minimally invasive off-pump beating heart mitral valve repair aims to deliver equivalent treatment for mitral regurgitation with reduced trauma and side effects. However, minimally invasive approaches are often limited by the lack of a direct view to surgical targets and/or tools, a challenge that is compounded by potential movement of the target during the cardiac cycle. For this reason, sophisticated image guidance systems are required in achieving procedural efficiency and therapeutic success. The development of such guidance systems is associated with many challenges. For example, the system should be able to provide high quality visualization of both cardiac anatomy and motion, as well as augmenting it with virtual models of tracked tools and targets. It should have the capability of integrating pre-operative images to the intra-operative scenario through registration techniques. The computation speed must be sufficiently fast to capture the rapid cardiac motion. Meanwhile, the system should be cost effective and easily integrated into standard clinical workflow. This thesis develops image processing techniques to address these challenges, aiming to achieve a safe and efficient guidance system for off-pump beating heart mitral valve repair. These techniques can be divided into two categories, using 3D and 2D image data respectively. When 3D images are accessible, a rapid multi-modal registration approach is proposed to link the pre-operative CT images to the intra-operative ultrasound images. The ultrasound images are used to display the real time cardiac motion, enhanced by CT data serving as high quality 3D context with annotated features. I also developed a method to generate synthetic dynamic CT images, aiming to replace real dynamic CT data in such a guidance system to reduce the radiation dose applied to the patients. When only 2D images are available, an approach is developed to track the feature of interest, i.e. the mitral annulus, based on bi-plane ultrasound images and a magnetic tracking system. The concept of modern GPU-based parallel computing is employed in most of these approaches to accelerate the computation in order to capture the rapid cardiac motion with desired accuracy. Validation experiments were performed on phantom, animal and human data. The overall accuracy of registration and feature tracking with respect to the mitral annulus was about 2-3mm with computation time of 60-400ms per frame, sufficient for one update per cardiac cycle. It was also demonstrated in the results that the synthetic CT images can provide very similar anatomical representations and registration accuracy compared to that of the real dynamic CT images. These results suggest that the approaches developed in the thesis have good potential for a safer and more effective guidance system for off-pump beating heart mitral valve repair

FASTR: Using Local Structure Tensors as a Similarity Metric

AbstractWe describe a novel structural image descriptor for image registration called the Fractionally Anisotropic Structural Tensor Representation (FASTR), calculated from the local structural tensor (LST). The metric has several characteristics that are advantageous for multi-modality registration, such as not depending on absolute voxel intensities, and being insensitive to slowly varying in- tensity inhomogeneities across the image. This latter property is very useful, since many imaging modalities suffer from such artefacts. Registration accuracy is tested on both computed tomography (CT) to cone-beam CT (CBCT) rigid registration, and CT to magnetic resonance (MR) rigid registration. The performance is compared with Mutual Information (MI) metric and the Self Similarity Context (SSC) descriptor. The results show that, for images with significant intensity inhomogeneity, FASTR produced more accurate results than MI, and faster results than SSC. The results suggest FASTR gives similar benefits in images with intensity inhomogeneity, but at a fraction of the computation and memory demand