Dense deformation field estimation for atlas registration using the active contour framework (2007)

A key research area in computer vision is image segmentation. Image segmentation aims at extracting objects of interest in images or video sequences. These objects contain relevant information for a given application. For example, a video surveillance application generally requires to extract moving objects (vehicles, persons or animals) from a sequence of images in order to check that their path stays conformed to the regulation rules set for the observed scene. Image segmentation is not an easy task. In many applications, the contours of the objects of interest are difficult to delineate, even manually. The problems linked to segmentation are often due to low contrast, fuzzy contours or too similar intensities with adjacent objects. In some cases, the objects to be extracted have no real contours in the image. This kind of objects is called virtual objects. Virtual objects appear especially in medical applications. To draw them, medical experts usually estimate their position from surrounding objects. The problems related to image segmentation can be greatly simplified with information known in advance on the objects to be extracted (the prior knowledge). A widely used method consists to extract the needed prior knowledge from a reference image often called atlas. The goal of the atlas is to describe the image to be segmented like a map would describe the components of a geographical area. An atlas can contain three types of information on each object being part of the image: an estimation of its position in the image, a description of its shape and texture, and the features of its adjacent objects. The atlas-based segmentation method is rather used when the atlas can characterize a range of images. This method is thus especially adapted to medical images due to the existing consistency between anatomical structures of same type. There exist two types of atlas: the determinist atlas and the statistical atlas. The determinist atlas is an image which has been selected or computed, to be the most representative of an image category to be segmented. This image is called intensity atlas. The contours of the objects of interest (the objects to be extracted in images of the same type) have been traced manually on the intensity atlas, or by using a semi-automatic method. A label is often attributed to each one of these objects in order to differentiate them. In this way, we obtain a labeled version of the atlas called labeled atlas. The statistical atlas is an atlas created from a database of images in order to be the most representative of a certain type of images to be segmented. In this atlas, the position and the features of the objects of interest depend on statistical measures. In this thesis, we are focused on the use of determinist atlases for image segmentation. The segmentation process with a determinist atlas consists to deform the objects delineated in the atlas in order to better align them with their corresponding objects in the image to be segmented. To perform this task, we have distinguished two types of approaches in the literature. The first approach consists to reduce the segmentation problem in an image registration problem. First of all, a dense deformation field that registers (i.e. puts in point-to-point spatial correspondence) the atlas to the image to be segmented, is explicitly computed. Then, this transformation is used to project the assigned labels onto each atlas structure on the image to be segmented. The advantage of this approach is that the deformation field computed from the registration of visible contours allows to easily estimate the position of virtual objects or objects with fuzzy contours. However, the methods currently used for the atlas registration are often only based on the intensity atlas. That means that they do not exploit the object-based information that can be obtained by combining the intensity atlas with its labeled version. In the second approach, the atlas contours selected by the labeled atlas are directly deformed without using a geometrical deformation. For that, this approach is based on matching contour techniques, generally called deformable models. In this thesis, we are interested to a particular type of deformable models, which are the active contour segmentation models. The advantage of the active contour method is that this segmentation technique has been designed to exploit the image information directly linked to the object to be delineated. By using object-based information, active contour models are frequently able to extract regions where the atlas-based segmentation method by registration fails. On the other hand, the result of this local segmentation method is very sensitive to the initial atlas contour position regarding to the target contours. On the other hand, this local segmentation method is very sensitive to the initial position of the atlas contours: the closer they are to the contours to be detected, the more robust the active contour-based segmentation will be. Besides, this segmentation technique needs prior shape models to be able to estimate the position of virtual objects. The main objective of this thesis is to design an algorithm for atlas-based segmentation which combines the advantages of the dense deformation field computed by the registration algorithms, with local segmentation constraints coming from the active contour framework. This implies to design a model where the registration and segmentation by active contours are jointly performed. The atlas registration algorithm that we propose is based on a formulation allowing the integration of any segmentation or contour regularization forces derived from the theory of the active contours in a non parametric registration process. Our algorithm led us to introduce the concept of hierarchical atlas registration. Its principle is that the registration of the main image objects helps the registration of depending objects. This allows to bring progressively the atlas contours closer to their target and thus, to limit the risk to be stuck in a local minimum. Our model had been designed to be easily adaptable to various types of segmentation problems. At the end of the thesis, we present several examples of atlas registration applications in medical imaging. These applications highlight the integration of manual constraints in an atlas registration process, the modeling of a tumor growth in the atlas, the labelization of the thalamus for a statistical study on neuronal connections, the localization of the subthalamic nucleus (STN) for deep brain stimulation (DBS) and the compensation of intra-operative brain shift for neuronavigation systems.