Knowledge Based Measurement Of Enhancing Brain Tissue In Anisotropic Mr Imagery

Medical Image Analysis has emerged as an important field in the computer vision community. In this thesis, two important issues in medical imaging are addressed and a solution for each is derived and synergistically combined as one coherent system. Firstly, a novel approach is proposed for High Resolution Volume (HRV) construction by combining different frequency components at multiple levels, which are separated by using a multi-resolution pyramid structure. Current clinical imaging protocols make use of multiple orthogonal low resolution scans to measure the size of the tumor. The highly anisotropic data result in difficulty and even errors in tumor assessment. In previous approaches, simple interpolation has been used to construct HRVs from multiple low resolution volumes (LRVs), which fail when large inter-plane spacing is present. In our approach, Laplacian pyramids containing band-pass contents are first computed from registered LRVs. The Laplacian images are expanded in their low resolution axes separately and then fused at each level. A Gaussian pyramid is recovered from the fused Laplacian pyramid, where a volume at the bottom level of the Gaussian pyramid is the constructed HRV. The effectiveness of the proposed approach is validated by using simulated images. The method has also been applied to real clinical data and promising experimental results are demonstrated. Secondly, a new knowledge-based framework to automatically quantify the volume of enhancing tissue in brain MR images is proposed. Our approach provides an objective and consistent way to evaluate disease progression and assess the treatment plan. In our approach, enhanced regions are first located by comparing the difference between the aligned set of pre- and post-contrast T1 MR images. Since some normal tissues may also become enhanced by the administration of Gd-DTPA, using the intensity difference alone may not be able to distinguish normal tissue from the tumor. Thus, we propose a new knowledge-based method employing knowledge of anatomical structures from a probabilistic brain atlas and the prior distribution of brain tumor to identify the real enhancing tissue. Our approach has two main advantages. i) The results are invariant to the image contrast change due to the usage of the probabilistic knowledge-based framework. ii) Using the segmented regions instead of independent pixels facilitates an approach that is much less sensitive to small registration errors and image noise. The obtained results are compared to the ground truth for validation and it is shown that the proposed method can achieve accurate and consistent measurements

A large margin algorithm for automated segmentation of white matter hyperintensity

Precise detection and quantification of white matter hyperintensity (WMH) is of great interest in studies of neurological and vascular disorders. In this work, we propose a novel method for automatic WMH segmentation with both supervised and semi-supervised large margin algorithms provided by the framework. The proposed algorithms optimize a kernel based max-margin objective function which aims to maximize the margin between inliers and outliers. We show that the semi-supervised learning problem can be formulated to learn a classifier and label assignment simultaneously, which can be solved efficiently by an iterative algorithm. The model is learned first via the supervised approach and then fine-tuned on a target image by using the semi-supervised algorithm. We evaluate our method on 88 brain fluid-attenuated inversion recovery (FLAIR) magnetic resonance (MR) images from subjects with vascular disease. Quantitative evaluation of the proposed approach shows that it outperforms other well known methods for WMH segmentation

Atlas-based segmentation and classification of magnetic resonance brain images

A wide range of different image modalities can be found today in medical imaging. These modalities allow the physician to obtain a non-invasive view of the internal organs of the human body, such as the brain. All these three dimensional images are of extreme importance in several domains of medicine, for example, to detect pathologies, follow the evolution of these pathologies, prepare and realize surgical planning with, or without, the help of robot systems or for statistical studies. Among all the medical image modalities, Magnetic Resonance (MR) imaging has become of great interest in many research areas due to its great spatial and contrast image resolution. It is therefore perfectly suited for anatomic visualization of the human body such as deep structures and tissues of the brain. Medical image analysis is a complex task because medical images usually involve a large amount of data and they sometimes present some undesirable artifacts, as for instance the noise. However, the use of a priori knowledge in the analysis of these images can greatly simplify this task. This prior information is usually represented by the reference images or atlases. Modern brain atlases are derived from high resolution cryosections or in vivo images, single subject-based or population-based, and they provide detailed images that may be interactively and easily examined in their digital format in computer assisted diagnosis or intervention. Then, in order to efficiently combine all this information, a battery of registration techniques is emerging based on transformations that bring two medical images into voxel-to-voxel correspondence. One of the main aims of this thesis is to outline the importance of including prior knowledge in the medical image analysis framework and the indispensable role of registration techniques in this task. In order to do that, several applications using atlas information are presented. First, the atlas-based segmentation in normal anatomy is shown as it is a key application of medical image analysis using prior knowledge. It consists of registering the brain images derived from different subjects and modalities within the atlas coordinate system to improve the localization and delineation of the structures of interest. However, the use of an atlas can be problematic in some particular cases where some structures, for instance a tumor or a sulcus, exists in the subject and not in the atlas. In order to solve this limitation of the atlases, a new atlas-based segmentation method for pathological brains is proposed in this thesis as well as a validation method to assess this new approach. Results show that deep structures of the brain can still be efficiently segmented using an anatomic atlas even if they are largely deformed because of a lesion. The importance of including a priori knowledge is also presented in the application of brain tissue classification. The prior information represented by the tissue templates can be included in a brain tissue segmentation approach thanks to the registration techniques. This is another important issue presented in this thesis and it is analyzed through a comparative study of several non-supervised classification techniques. These methods are selected to represent the whole range of prior information that can be used in the classification process: the image intensity, the local spatial model, and the anatomical priors. Results show that the registration between the subject and the tissue templates allows the use of prior information but the accuracy of both the prior information and the registration highly influence the performance of the classification techniques. Another aim of this thesis is to present the concept of dynamic medical image analysis, in which the prior knowledge and the registration techniques are also of main importance. Actually, many medical image applications have the objective of statically analyzing one single image, as for instance in the case of atlas-based segmentation or brain tissue classification. But in other cases the implicit idea of changes detection is present. Intuitively, since the human body is changing continuously, we would like to do the image analysis from a dynamic point of view by detecting these changes, and by comparing them afterwards with templates to know if they are normal. The need of such approaches is even more evident in the case of many brain pathologies such as tumors, multiple sclerosis or degenerative diseases. In these cases, the key point is not only to detect but also to quantify and even characterize the evolving pathology. The evaluation of lesion variations over time can be very useful, for instance in the pharmaceutical research and clinical follow up. Of course, a sequence of images is needed in order to do such an analysis. Two approaches dealing with the idea of change detection are proposed as the last (but not least) issue presented in this work. The first one consists of performing a static analysis of each image forming the data set and, then, of comparing them. The second one consists of analyzing the non-rigid transformation between the sequence images instead of the images itself. Finally, both static and dynamic approaches are illustrated with a potential application: the cortical degeneration study is done using brain tissue segmentation, and the study of multiple sclerosis lesion evolution is performed by non-rigid deformation analysis. In conclusion, the importance of including a priori information encoded in the brain atlases in medical image analysis has been put in evidence with a wide range of possible applications. In the same way, the key role of registration techniques is shown not only as an efficient way to combine all the medical image modalities but also as a main element in the dynamic medical image analysis

Radiotherapy planning for glioblastoma based on a tumor growth model: Improving target volume delineation

Glioblastoma are known to infiltrate the brain parenchyma instead of forming a solid tumor mass with a defined boundary. Only the part of the tumor with high tumor cell density can be localized through imaging directly. In contrast, brain tissue infiltrated by tumor cells at low density appears normal on current imaging modalities. In clinical practice, a uniform margin is applied to account for microscopic spread of disease. The current treatment planning procedure can potentially be improved by accounting for the anisotropy of tumor growth: Anatomical barriers such as the falx cerebri represent boundaries for migrating tumor cells. In addition, tumor cells primarily spread in white matter and infiltrate gray matter at lower rate. We investigate the use of a phenomenological tumor growth model for treatment planning. The model is based on the Fisher-Kolmogorov equation, which formalizes these growth characteristics and estimates the spatial distribution of tumor cells in normal appearing regions of the brain. The target volume for radiotherapy planning can be defined as an isoline of the simulated tumor cell density. A retrospective study involving 10 glioblastoma patients has been performed. To illustrate the main findings of the study, a detailed case study is presented for a glioblastoma located close to the falx. In this situation, the falx represents a boundary for migrating tumor cells, whereas the corpus callosum provides a route for the tumor to spread to the contralateral hemisphere. We further discuss the sensitivity of the model with respect to the input parameters. Correct segmentation of the brain appears to be the most crucial model input. We conclude that the tumor growth model provides a method to account for anisotropic growth patterns of glioblastoma, and may therefore provide a tool to make target delineation more objective and automated

Atlas-Based Segmentation of Pathological Brain MR Images

We propose a method for brain atlas deformation in presence of large space-occupying tumors, based on an a priori model of lesion growth that assumes radial expansion of the lesion from its starting point. First, an affine registration brings the atlas and the patient into global correspondence. Then, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. Finally, the seeded atlas is deformed, combining a method derived from optical flow principles and a model of lesion growth (MLG). Results show that the method can be applied to the automatic segmentation of structures and substructures in brains with gross deformation, with important medical applications in neurosurgery, radiosurgery and radiotherapy