A GPU framework for parallel segmentation of volumetric images using discrete deformable models

Despite the ability of current GPU processors to treat heavy parallel computation tasks, its use for solving medical image segmentation problems is still not fully exploited and remains challenging. A lot of difficulties may arise related to, for example, the different image modalities, noise and artifacts of source images, or the shape and appearance variability of the structures to segment. Motivated by practical problems of image segmentation in the medical field, we present in this paper a GPU framework based on explicit discrete deformable models, implemented over the NVidia CUDA architecture, aimed for the segmentation of volumetric images. The framework supports the segmentation in parallel of different volumetric structures as well as interaction during the segmentation process and real-time visualization of the intermediate results. Promising results in terms of accuracy and speed on a real segmentation experiment have demonstrated the usability of the syste

A GPU framework for parallel segmentation of volumetric images using discrete deformable models

Despite the ability of current GPU processors to treat heavy parallel computation tasks, its use for solving medical image segmentation problems is still not fully exploited and remains challenging. A lot of difficulties may arise related to, for example, the different image modalities, noise and artifacts of source images, or the shape and appearance variability of the structures to segment. Motivated by practical problems of image segmentation in the medical field, we present in this paper a GPU framework based on explicit discrete deformable models, implemented over the NVidia CUDA architecture, aimed for the segmentation of volumetric images. The framework supports the segmentation in parallel of different volumetric structures as well as interaction during the segmentation process and real-time visualization of the intermediate results. Promising results in terms of accuracy and speed on a real segmentation experiment have demonstrated the usability of the system.85-95Pubblicat

Development of an Atlas-Based Segmentation of Cranial Nerves Using Shape-Aware Discrete Deformable Models for Neurosurgical Planning and Simulation

Twelve pairs of cranial nerves arise from the brain or brainstem and control our sensory functions such as vision, hearing, smell and taste as well as several motor functions to the head and neck including facial expressions and eye movement. Often, these cranial nerves are difficult to detect in MRI data, and thus represent problems in neurosurgery planning and simulation, due to their thin anatomical structure, in the face of low imaging resolution as well as image artifacts. As a result, they may be at risk in neurosurgical procedures around the skull base, which might have dire consequences such as the loss of eyesight or hearing and facial paralysis. Consequently, it is of great importance to clearly delineate cranial nerves in medical images for avoidance in the planning of neurosurgical procedures and for targeting in the treatment of cranial nerve disorders. In this research, we propose to develop a digital atlas methodology that will be used to segment the cranial nerves from patient image data. The atlas will be created from high-resolution MRI data based on a discrete deformable contour model called 1-Simplex mesh. Each of the cranial nerves will be modeled using its centerline and radius information where the centerline is estimated in a semi-automatic approach by finding a shortest path between two user-defined end points. The cranial nerve atlas is then made more robust by integrating a Statistical Shape Model so that the atlas can identify and segment nerves from images characterized by artifacts or low resolution. To the best of our knowledge, no such digital atlas methodology exists for segmenting nerves cranial nerves from MRI data. Therefore, our proposed system has important benefits to the neurosurgical community

Evolution of surface-based deformable image registration for adaptive radiotherapy of non-small cell lung cancer (NSCLC)

<p>Abstract</p> <p>Background</p> <p>To evaluate the performance of surface-based deformable image registration (DR) for adaptive radiotherapy of non-small cell lung cancer (NSCLC).</p> <p>Methods</p> <p>Based on 13 patients with locally advanced NSCLC, CT images acquired at treatment planning, midway and the end of the radio- (n = 1) or radiochemotherapy (n = 12) course were used for evaluation of DR. All CT images were manually [gross tumor volume (GTV)] and automatically [organs-at-risk (OAR) lung, spinal cord, vertebral spine, trachea, aorta, outline] segmented. Contours were transformed into 3D meshes using the Pinnacle treatment planning system and corresponding mesh points defined control points for DR with interpolation within the structures. Using these deformation maps, follow-up CT images were transformed into the planning images and compared with the original planning CT images.</p> <p>Results</p> <p>A progressive tumor shrinkage was observed with median GTV volumes of 170 cm³(range 42 cm³- 353 cm³), 124 cm³(19 cm³- 325 cm³) and 100 cm³(10 cm³- 270 cm³) at treatment planning, mid-way and at the end of treatment. Without DR, correlation coefficients (CC) were 0.76 ± 0.11 and 0.74 ± 0.10 for comparison of the planning CT and the CT images acquired mid-way and at the end of treatment, respectively; DR significantly improved the CC to 0.88 ± 0.03 and 0.86 ± 0.05 (p = 0.001), respectively. With manual landmark registration as reference, DR reduced uncertainties on the GTV surface from 11.8 mm ± 5.1 mm to 2.9 mm ± 1.2 mm. Regarding the carina and intrapulmonary vessel bifurcations, DR reduced uncertainties by about 40% with residual errors of 4 mm to 6 mm on average. Severe deformation artefacts were observed in patients with resolving atelectasis and pleural effusion, in one patient, where the tumor was located around large bronchi and separate segmentation of the GTV and OARs was not possible, and in one patient, where no clear shrinkage but more a decay of the tumor was observed.</p> <p>Discussion</p> <p>The surface-based DR performed accurately for the majority of the patients with locally advanced NSCLC. However, morphological response patterns were identified, where results of the surface-based DR are uncertain.</p

Deformable meshes for shape recovery: models and applications

With the advance of scanning and imaging technology, more and more 3D objects become available. Among them, deformable objects have gained increasing interests. They include medical instances such as organs, a sequence of objects in motion, and objects of similar shapes where a meaningful correspondence can be established between each other. Thus, it requires tools to store, compare, and retrieve them. Many of these operations depend on successful shape recovery. Shape recovery is the task to retrieve an object from the environment where its geometry is hidden or implicitly known. As a simple and versatile tool, mesh is widely used in computer graphics for modelling and visualization. In particular, deformable meshes are meshes which can take the deformation of deformable objects. They extend the modelling ability of meshes. This dissertation focuses on using deformable meshes to approach the 3D shape recovery problem. Several models are presented to solve the challenges for shape recovery under different circumstances. When the object is hidden in an image, a PDE deformable model is designed to extract its surface shape. The algorithm uses a mesh representation so that it can model any non-smooth surface with an arbitrary precision compared to a parametric model. It is more computational efficient than a level-set approach. When the explicit geometry of the object is known but is hidden in a bank of shapes, we simplify the deformation of the model to a graph matching procedure through a hierarchical surface abstraction approach. The framework is used for shape matching and retrieval. This idea is further extended to retain the explicit geometry during the abstraction. A novel motion abstraction framework for deformable meshes is devised based on clustering of local transformations and is successfully applied to 3D motion compression

A review of segmentation and deformable registration methods applied to adaptive cervical cancer radiation therapy treatment planning

Objective: Manual contouring and registration for radiotherapy treatment planning and online adaptation for cervical cancer radiation therapy in computed tomography (CT) and magnetic resonance images (MRI) are often necessary. However manual intervention is time consuming and may suffer from inter or intra-rater variability. In recent years a number of computer-guided automatic or semi-automatic segmentation and registration methods have been proposed. Segmentation and registration in CT and MRI for this purpose is a challenging task due to soft tissue deformation, inter-patient shape and appearance variation and anatomical changes over the course of treatment. The objective of this work is to provide a state-of-the-art review of computer-aided methods developed for adaptive treatment planning and radiation therapy planning for cervical cancer radiation therapy. Methods: Segmentation and registration methods published with the goal of cervical cancer treatment planning and adaptation have been identified from the literature (PubMed and Google Scholar). A comprehensive description of each method is provided. Similarities and differences of these methods are highlighted and the strengths and weaknesses of these methods are discussed. A discussion about choice of an appropriate method for a given modality is provided. Results: In the reviewed papers a Dice similarity coefficient of around 0.85 along with mean absolute surface distance of 2-4. mm for the clinically treated volume were reported for transfer of contours from planning day to the treatment day. Conclusions: Most segmentation and non-rigid registration methods have been primarily designed for adaptive re-planning for the transfer of contours from planning day to the treatment day. The use of shape priors significantly improved segmentation and registration accuracy compared to other models

Multi-Surface Simplex Spine Segmentation for Spine Surgery Simulation and Planning

This research proposes to develop a knowledge-based multi-surface simplex deformable model for segmentation of healthy as well as pathological lumbar spine data. It aims to provide a more accurate and robust segmentation scheme for identification of intervertebral disc pathologies to assist with spine surgery planning. A robust technique that combines multi-surface and shape statistics-aware variants of the deformable simplex model is presented. Statistical shape variation within the dataset has been captured by application of principal component analysis and incorporated during the segmentation process to refine results. In the case where shape statistics hinder detection of the pathological region, user-assistance is allowed to disable the prior shape influence during deformation. Results have been validated against user-assisted expert segmentation

Statistical Medial Model dor Cardiac Segmentation and Morphometry

In biomedical image analysis, shape information can be utilized for many purposes. For example, irregular shape features can help identify diseases; shape features can help match different instances of anatomical structures for statistical comparison; and prior knowledge of the mean and possible variation of an anatomical structure\u27s shape can help segment a new example of this structure in noisy, low-contrast images. A good shape representation helps to improve the performance of the above techniques. The overall goal of the proposed research is to develop and evaluate methods for representing shapes of anatomical structures. The medial model is a shape representation method that models a 3D object by explicitly defining its skeleton (medial axis) and deriving the object\u27s boundary via inverse-skeletonization . This model represents shape compactly, and naturally expresses descriptive global shape features like thickening , bending , and elongation . However, its application in biomedical image analysis has been limited, and it has not yet been applied to the heart, which has a complex shape. In this thesis, I focus on developing efficient methods to construct the medial model, and apply it to solve biomedical image analysis problems. I propose a new 3D medial model which can be efficiently applied to complex shapes. The proposed medial model closely approximates the medial geometry along medial edge curves and medial branching curves by soft-penalty optimization and local correction. I further develop a scheme to perform model-based segmentation using a statistical medial model which incorporates prior shape and appearance information. The proposed medial models are applied to a series of image analysis tasks. The 2D medial model is applied to the corpus callosum which results in an improved alignment of the patterns of commissural connectivity compared to a volumetric registration method. The 3D medial model is used to describe the myocardium of the left and right ventricles, which provides detailed thickness maps characterizing different disease states. The model-based myocardium segmentation scheme is tested in a heterogeneous adult MRI dataset. Our segmentation experiments demonstrate that the statistical medial model can accurately segment the ventricular myocardium and provide useful parameters to characterize heart function

Automatic Mesh-Based Segmentation of Multiple Organs in MR Images

La segmentation de structures anatomiques multiples dans des images de résonance magnétique (RM) est souvent requise dans des applications de génie biomédical telles que la simulation numérique, la chirurgie guidée par l’image, la planification de traitements, etc. De plus, il y a un besoin croissant pour une segmentation automatique d’organes multiples et de structures complexes à partir de cette modalité d’imagerie. Il existe plusieurs techniques de segmentation multi-objets qui ont été appliquées avec succès sur des images de tomographie axiale à rayons-X (CT). Cependant, dans le cas des images RM cette tâche est plus difficile en raison de l’inhomogénéité des intensités dans ces images et de la variabilité dans l’apparence des structures anatomiques. Par conséquent, l’état de l’art sur la segmentation multi-objets sur des images RM est beaucoup plus faible que celui sur les images CT. Parmi les travaux qui portent sur la segmentation d’images RM, les approches basées sur la segmentation de régions sont sensibles au bruit et la non uniformité de l’intensité dans les images. Les approches basées sur les contours ont de la difficulté à regrouper les informations sur les contours de sorte à produire un contour fermé cohérent. Les techniques basées sur les atlas peuvent avoir des problèmes en présence de structures complexes avec une grande variabilité anatomique. Les modèles déformables représentent une des méthodes les plus populaire pour la détection automatique de différents organes dans les images RM. Cependant, ces modèles souffrent encore d’une limitation importante qui est leur sensibilité à la position initiale et la forme du modèle. Une initialisation inappropriée peut conduire à un échec dans l’extraction des frontières des objets. D’un autre côté, le but ultime d’une segmentation automatique multi-objets dans les images RM est de produire un modèle qui peut aider à extraire les caractéristiques structurelles d’organes distincts dans les images. Les méthodes d’initialisation automatique actuelles qui utilisent différents descripteurs ne réussissent pas complètement l’extraction d’objets multiples dans les images RM. Nous avons besoin d’exploiter une information plus riche qui se trouve dans les contours des organes. Dans ce contexte les maillages adaptatifs anisotropiques semblent être une solution potentielle au problème soulevé. Les maillages adaptatifs anisotropiques construits à partir des images RM contiennent de l’information à un plus haut niveau d’abstraction représentant les éléments, d’une orientation et d’une forme donnée, qui constituent les différents organes dans l’image. Les méthodes existantes pour la construction de maillages adaptatifs sont basées sur les intensités dans l’image et possèdent une limitation pratique qui est l’alignement inadéquat des éléments du maillage en présence de contours inclinés dans l’image. Par conséquent, nous avons aussi besoin d’améliorer le processus d’adaptation de maillage pour produire une meilleure représentation de l’image basée sur un maillage.----------ABSTRACT: Segmentation of multiple anatomical structures in MR images is often required for biomedical engineering applications such as clinical simulation, image-guided surgery, treatment planning, etc. Moreover, there is a growing need for automatic segmentation of multiple organs and complex structures from this medical imaging modality. Many successful multi-object segmentation attempts were introduced for CT images. However in the case of MR images it is a more challenging task due to intensity inhomogeneity and variability of anatomy appearance. Therefore, state-of-the-art in multi-object MR segmentation is very inferior to that of CT images. In literature dealing with MR image segmentation, the region-based approaches are sensitive to noise and non-uniformity in the input image. The edge-based approaches are challenging to group the edge information into a coherent closed contour. The atlas-based techniques can be problematic for complicated structures with anatomical variability. Deformable models are among the most popular methods for automatic detection of different organs in MR images. However they still have an important limitation which is that they are sensitive to initial position and shape of the model. An unsuitable initialization may provide failure to capture the true boundaries of the objects. On the other hand, a useful aim for an automatic multi-object MR segmentation is to provide a model which promotes understanding of the structural features of the distinct objects within the MR images. The current automatic initialization methods which have used different descriptors are not completely successful in extracting multiple objects from MR images and we need to find richer information that is available from edges. In this regard, anisotropic adaptive meshes seem to be a potential solution to the aforesaid limitation. Anisotropic adaptive meshes constructed from MR images contain higher level, abstract information about the anatomical structures of the organs within the image retained as the elements shape and orientation. Existing methods for constructing adaptive meshes based on image features have a practical limitation where manifest itself in inadequate mesh elements alignment to inclined edges in the image. Therefore, we also have to enhance mesh adaptation process to provide a better mesh-based representation. In this Ph.D. project, considering the highlighted limitations we are going to present a novel method for automatic segmentation of multiple organs in MR images by incorporating mesh adaptation techniques. In our progress, first, we improve an anisotropic adaptation process for the meshes that are constructed from MR images where the mesh elements align adequately to the image content and improve mesh anisotropy along edges in all directions. Then the resulting adaptive meshes are used for initialization of multiple active models which leads to extract initial object boundaries close to the true boundaries of multiple objects simultaneously. Finally, the Vector Field Convolution method is utilized to guide curve evolution towards the object boundaries to obtain the final segmentation results and present a better performance in terms of speed and accuracy