En orthodontie, le diagnostic et la planification d'un traitement reposent sur la connaissance de l'architecture dentaire du patient relevée, entre autre, par un moulage en plâtre. Aujourd’hui, des logiciels permettent de manipuler des modèles numériques des arcades dentaires obtenus après numérisation des moulages. Afin d’observer l’engrènement des dents, il est nécessaire de mettre en occlusion les deux arcades numérisées séparément. Cette étape est actuellement manuelle et l’objet de ces travaux de thèse est de proposer une chaîne robuste de traitements permettant un recalage automatique des deux arcades guidé par plusieurs photos "en bouche" du patient. L'approche proposée consiste à définir trois types de points singuliers et à mettre en place des méthodes robustes de détection automatique à la fois sur les modèles 3D et les images couleur s’appuyant sur la courbure et la texture. Une fois mis en correspondance, ces points homologues 2D/3D permettent d'estimer les matrices de projection puis la transformation rigide (6ddl) pour positionner au mieux la mandibule par rapport au maxillaire en minimisant les erreurs de reprojection dans plusieurs vues. Afin de s’affranchir du bruit de détection, les positions 2D et/ou 3D des points sont améliorées au cours du processus d’optimisation. De nombreux tests sur des données virtuelles et réelles valident l'approche choisie. L’occlusion finale obtenue par recalage automatique est proche de la référence de l’expert. Les résultats sont encourageants pour fournir une alternative automatique à intégrer dans un outil d'aide au diagnostic. / In orthodontics, the diagnosis and the planning of a treatment rest on the knowledge of the dental architecture of the patient using, among others, a dental cast in plaster. Today, dedicated software allow to manipulate digital models of the dental arches obtained after digitalization of the casts. To observe the contact of teeth, it is necessary to register both arches scanned separately. This stage is at present manual and the object of this thesis research is to propose a robust chain processing allowing an automatic registration of both arches guided by several photos of the patient mouth. The proposed approach consists in defining three types of singular points and in setting up strong methods of automatic detection at the same time on the 3D models and the color images leaning on the curvature and the texture. Once put in correspondence, these 2D / 3D equivalent points allow to estimate the projection matrices then the rigid transformation (6ddl) to position at best the mandible in relation to the maxillary by minimizing the reprojection errors in several views. To free itself from the noise of detection, the 2D and/or 3D positions of the singular points are improved during the optimization process. Numerous tests on virtual and real data validate the proposed approach. The final occlusion obtained on the real data by automatic registration is close to the reference of the expert. These are encouraging results to supply an automatic alternative to be integrated into a help tool for the diagnosis.

Le projet se situe dans le contexte de la gonarthrose fémoro-tibiale, et plus spécifiquement de son traitement par orthèse de décharge. Du fait de la cinématique particulière de l’orthèse testée, un protocole spécifique a été mis en place dans le but d’approfondir les mécanismes d’actions de cette orthèse. Ce protocole s’est appuyé sur des outils d’investigation utilisés dans la routine clinique (système EOS® et Vicon®). Seize sujets symptomatiques ont participé à l’étude. Les objectifs principaux étaient de valider et d’utiliser des méthodes de personnalisation des modèles, support de la biomécanique, dans ce contexte spécifique, afin d’améliorer la précision de la quantification des paramètres cinématiques et dynamiques. En effet, l’état de l’art démontre que l’indicateur dynamique couramment utilisé dans l’étude de la gonarthrose, le moment articulaire externe d’adduction, souffre de résultats controversés. Les objectifs secondaires étaient de caractériser la pathologie à l’aide des indicateurs calculés ainsi que d’approfondir le mécanisme d’action de l’orthèse de décharge. Ainsi, deux méthodes principales ont été investiguées. La première porte sur l’analyse séquentielle cinématique de l’articulation fémoro-tibiale en utilisant le système EOS®. Cette analyse nécessite une étape de recalage d’objet 3D sur des vues 2D biplanaires. La fiabilité de ce recalage manuel a été quantifiée en évaluant, d’une part, la précision de la méthode grâce à des données in vitro et, d’autre part, la répétabilité de la méthode grâce à la participation de 3 opérateurs et de 6 sujets asymptomatiques dont les acquisitions ont permis d’obtenir des vues du genou dans plusieurs positions (extension et flexion 20°, 40°et 90°). La seconde méthode consiste en la fusion de données issues de deux environnements (EOS® et Vicon®) de façon à quantifier les moments articulaires externes dans le genou en définissant le point auquel sont calculés ces moments à partir du modèle 3D du fémur. Ce modèle étant recalé dans l’environnement Vicon® par l’intermédiaire des marqueurs externes détectables dans les acquisitions EOS® et Vicon®. Les résultats principaux concernent :1/ la fiabilité du recalage des modèles 3D des os sur des vues 2D de l’ordre de 0,3° et 1,6 mm dans le plan sagittal de 2,1° et 1,8mm dans le plan transversal ; 2/ la quantification d’angles positionnels 3D du fémur et du tibia des membres inférieurs symptomatiques montrant que la surface articulaire tibiale (plateaux tibiaux) tend à demeurer horizontale contrairement à l’inclinaison plus marquée du fémur ; 3/ une variation des moments articulaires externes en fonction de l’intégration ou non d’un modèle interne pour le calcul de ce paramètre ; 4/ la quantification de la cinématique séquentielle de l’orthèse et du genou. La fiabilité des méthodes développées dans ce travail a été estimée ouvrant la voie à leurs applications et à leurs développements en clinique.Mots clés : gonarthrose fémoro-tibiale ; orthèse ; analyse séquentielle ; recalage. / The context is the knee osteoarthritis and its treatment via an unloading brace. As the evaluated brace has specific kinematics, a dedicated protocol was set up using clinical routine tools (EOS® and Vicon®). Sixteen symptomatic subjects participated to this study. The main objective was to validate and to use personalization methods of the biomechanical models to improve the accuracy kinematics and kinetics parameter computation in this specific context. Indeed, the state of the art highlights that the dynamic indicator, currently used in knee osteoarthritis studies, the external adduction joint moment is controversial. The secondary objectives were both the characterization of the pathology using indicators obtained on the acquired data and the in-depth study of the mechanical action of the unloading brace evaluated in this study. Thus, two main methods were investigated. The first one is the sequential analysis of the knee kinematics using EOS® system. This analysis required a registration step of a 3D object on 2D biplanar views. The manual registration reliability was quantified by evaluating both the method accuracy with in-vitro data and the method repeatability thanks to the participation of 3 operators and 6 asymptomatic subjects allowing the acquisition of knee images in several positions (extension and 20°, 40°, and 90° flexion). The second method consists in the fusion of data obtained in the two acquisitions environments (EOS® and Vicon®), to obtain the external knee joint moment in order to define the point where the moment is computed from the femur 3D model. This model is registered in the Vicon® environment through external markers visible in both the EOS® and Vicon® acquisitions. The main results relate to: 1/the reliability of the registration of the bone 3D model on 2D views estimated at about 0,3° and 1,6 mm in the sagittal plane and about 2,1° and 1,8 mm in the transverse plane ; 2/ the quantification of the angular relative position of the shank and tibia of the symptomatic lower limbs, showing the tibial plateau horizontality opposed to the femur emphasized inclination ; 3/ external joint moment variation according to the computation method (with or without internal model included) ; 4/ brace and knee sequential kinematic quantification. As the reliability of the methods developed in this study was estimated, further developments and clinical applications and development could now be explored using these methods.Keywords : knee osteoarthritis; brace, sequential analysis; registration.

Anatomic changes occur throughout head and neck radiotherapy, and a new treatment plan is often required to mitigate the resulting changes in delivered dose to key structures. This process is known as adaptive radiotherapy (ART), and can be labour-intensive. The aim of this thesis is to optimise ART, addressing some of the technical and clinical challenges facing its routine clinical implementation. Optimising the frequency and timing of adaptive replanning is important, and it has been shown here that intensity modulated radiotherapy (IMRT) and volumetric modulated arc therapy (VMAT) are equally robust to weight loss during head and neck radiotherapy. Plan adaptation strategies that have previously been developed for IMRT are therefore applicable to VMAT.Contour propagation is an important component of ART, and it is essential to ensure that propagated contours are accurate. A method for assessing the suitability of a metric for measuring automatic segmentation accuracy has been developed and applied to the head and neck. For the parotids and larynx, metrics based on surface agreement were better than the commonly used Dice similarity coefficient. By establishing a consensus on which metrics should be used to assess segmentation accuracy, comparison of different algorithms is more objective and should lead to more accurate automatic segmentation. A novel method of assessing contour propagation accuracy on a patient-specific basis has also been developed. This was demonstrated on a cohort of head and neck patients and shows potential as a tool for identifying propagated contours that are subject to a high degree of uncertainty. This is a novel tool that will increase the efficiency of automatic segmentation and, therefore, ART.Optimum ART requires consideration of different radiotherapy-related toxicities, and image-based data mining is a powerful technique for spatially localising dose-response relationships. Correction for multiple comparisons through permutation testing is essential, but has so far only been applied to categorical data. A novel method has been developed for performing permutation testing and image-based data mining with a continuously variable clinical endpoint. Application to trismus for head and neck radiotherapy identified a region with a dose-response relationship in the ipsilateral masseter. Sparing this structure during radiotherapy should reduce the severity of radiation-induced trismus. ART mitigates the dosimetric effects of anatomic changes, and this thesis has addressed technical and clinical challenges that have so far limited its clinical implementation. Detailed knowledge of dose-response relationships will enable selection of patients for ART based on potential clinical benefit, and accurate contour propagation will make ART more efficient, facilitating its routine implementation.

This dissertation focuses on two distinct but related problems involving detection in multiple images. The first problem focuses on the accurate detection of runways by fusing Synthetic Vision System (SVS) and Enhanced Vision System (EVS) images. A novel procedure is developed to accurately detect runways and horizons and also enhance runway surrounding areas by fusing enhanced vision system (EVS) and synthetic vision system (SVS) images of the runway while an aircraft is landing. Because the EVS and SVS frames are not aligned, a registration step is introduced to align the EVS and SVS images prior to fusion. The most notable feature of the registration procedure is that it is guided by the information extracted from the weather-invariant SVS images. Four fusion rules based on combining Discrete Wavelet Transform (DWT) sub-bands are implemented and evaluated. The resulting procedure is tested on real EVS-SVS image pairs and also on image pairs containing simulated EVS images with varying levels of turbulence. The subjective and objective evaluations reveal that runways and horizons can be detected accurately even in poor visibility conditions. Furthermore, it is demonstrated that different aspects of the EVS and SVS images can be emphasized by using different DWT fusion rules. Another notable feature is that the entire procedure is autonomous throughout the landing sequence irrespective of the weather conditions. Given the excellent fusion results and the autonomous feature, it can be concluded that the fusion procedure developed is quite promising for incorporation into head-up displays (HUDs) to assist pilots in safely landing aircrafts in varying weather conditions. The second problem focuses on the blind detection of hidden messages that are embedded in images using various steganography methods. A new steganalysis strategy is introduced to blindly detect hidden messages that have been embedded in JPEG images using various steganography techniques. The key contribution is the formulation of a multi-domain feature extraction, ranking, and selection strategy to improve the steganalysis performance. The multi-domain features are statistical measures extracted from DWT, muti-wavelet (MWT), and slantlet (SLT) transforms. Feature ranking and selection is based on evaluating the performance of each feature independently and combining the best uncorrelated features. The resulting feature set is used in conjunction with discriminant analysis and support vector classifiers to detect the presence/absence of hidden messages in images. Numerous experiments are conducted to demonstrate the improved performance of the new steganalysis strategy over existing steganalysis methods.

O setor público brasileiro tem grande influência na economia, considerando o volume de tributos que arrecada e também pelo volume de bens públicos que administra, os quais, em matéria contábil, em parte, representam ativos patrimoniais. Este trabalho teve como objetivo propor um modelo de identificação e de classificação de Ativos para as entidades do setor público, harmonizando os conceitos constitucionais, legais e normativos, especialmente com as Normas Brasileiras de Contabilidade Aplicáveis ao Setor Público. Procurou-se evidenciar a possível convergência de conceitos de Ativos para entidades do setor público, as definições de bens da União e dos Estados, assim definidos no artigo 20 e 31 da Constituição Federal de 1988, bem como a convergência de conceitos de Ativos de entidades setor privado para com os de bens públicos. Para tanto, realizou-se uma revisão bibliográfica quanto à conceituação de bens, de bens públicos, de ativos e do patrimônio público, previstas nos diversos regramentos constitucionais e legais do país e na literatura. O trabalho resultou na identificação das diversas classes de ativos públicos, na estruturação de um modelo de identificação e classificação dos bens, com exemplos de utilização, visando a facilitar e qualificar os procedimentos de registro e o relevo dos bens públicos. O que, o caso, poderá ser útil para o entendimento dos eventos contábeis relacionados à identificação e sua classificação. / The Brazilian public sector has great influence on the economy, considering the amount of taxes it collects, and also by the volume of public goods that manages, which in accounting matters partly represent corporate assets. This study aimed to propose a model for the identification and classification of assets for the public sector entities, harmonizing the constitutional, legal and regulatory concepts, especially with the Brazilian Accounting Standards applicable to the Public Sector. It was essayed to evidence the possible convergence of Assets concepts for public sector entities to the (União) Federal Government and States assets definitions, as delineated in the Article 20 and 31 of the 1988’s Federal Constitution and the convergence of assets concepts of entities from private sector towards public goods. For that a literature review was conducted on the concept of goods, public goods, assets and public property, under the various constitutional and legal specific regulations of the country and in the literature. The work resulted in the identification of several classes of public assets and in the structuring of a model for identification and classification of goods, with examples of use, in order to facilitate and qualify registration procedures and disclosure of public goods, which could be useful for the understanding of accounting events related to their identification and classification.

A significant landscape element is a tool of general protection of the nature and landscape, the announcement of which is formally one of the fastest and easiest ways to protect. Act No. 114/1992 Coll. represents basic legislative document where is significant landscape element defined as an environmentally, geomorphologically or aesthetically valuable part of the landscape, which shapes its typical appearance or contributes to the maintenance of its stability. The theme of my thesis was the mapping of important landscape elements and the proposal for registration of a new significant landscape element in Pelhřimov area. Four cadastral territories were selected, in which significant landscape features were characterized. In the area of interest it was selected 4 registered significant landscape elements and 13 significant landscape elements of the law, which were divided into subcategories of watercourses, ponds and forests.

Le cancer de la prostate est le cancer le plus fréquent chez l'homme en France et aux pays occidentaux. Il est la troisième cause de décès liés au cancer, étant responsable d'environ 10% des morts. La curiethérapie, une technique de radiothérapie, est liée à une meilleure qualité de vie après le traitement, par rapport aux autres méthodes de traitement. La curiethérapie de la prostate consiste à insérer des sources radioactives dans la prostate afin de délivrer une dose d'irradiation localisée à la tumeur tout en protégeant les tissus sains environnants. L'imagerie multimodale est utilisée afin d'améliorer la précision du traitement. Les images Tomodensitométriques préopératoires, appelées Computed Tomography (CT), peuvent être utilisées pour calculer une distribution personnalisée et plus précise de dose. Pendant l'intervention, le chirurgien utilise un système de guidage temps-réel par l'Ultrason Transrectale, Transrectal Ultrasound (TRUS), pour placer correctement les sources radioactives dans leurs positions souhaitées. Par conséquent, si les positions des sources sont déterminées sur l'image CT, elles doivent être transférées à l'image US. Cependant, un recalage US/CT direct et robuste est difficilement envisageable parce que les tissus mous, telle que la prostate, offrent peu de contraste en CT et en US. En revanche, l'Imagerie par Résonance Magnétique (IRM) fournit un meilleur contraste et peut, potentiellement, améliorer le traitement en améliorant la visualisation. Donc, ces trois modalités (IRM, CT et US) doivent être correctement alignées. Pour compenser les déformations de la prostate, due au changement de taille et forme entre les différentes acquisitions, un recalage non-rigide est nécessaire. Une méthode de recalage entièrement automatique est nécessaire, afin de faciliter son intégration au bloc opératoire. Nous proposons dans un premier temps un recalage IRM/CT basé sur la maximisation de l'information mutuelle en combinaison avec un champ de déformation paramétré par B-Splines. Nous proposons de contraindre le recalage sur des volumes d'intérêt (VOIs) afin d'améliorer la robustesse et le temps de calcul. L'approche proposée a été validée sur des jeux de données cliniques. Une évaluation quantitative a montré que l'erreur de recalage est égale à 1.15±0.20 mm; qui répond à la précision clinique souhaitée. Ensuite, nous proposons un deuxième recalage US/IRM, où nous utilisons une approche multi-résolution pour éviter les minima locaux et améliorer le temps de calcul. Un critère de similarité, qui met en corrélation l'intensité de l'image US avec l'intensité ainsi que le gradient de l'image IRM, a été utilisé afin de trouver la transformation qui aligne les deux images. Cette méthode a été validée sur un fantôme de prostate dans un premier temps pour évaluer sa faisabilité. Ensuite, elle a été validée sur des jeux de données cliniques en utilisant des critères qualitatives et quantitatives. La distance Hausdorff a montré que l'erreur de recalage est égale à 1.44±0.06 mm. L'approche proposée dans ce travail permet d'aller vers un protocole de curiethérapie guidée par l'imagerie multimodale qui puisse améliorer la précision globale de cette procédure. Malgré ces résultats plutôt encourageants, les travaux futurs impliqueront une évaluation plus approfondie sur plus de jeux de données afin d'évaluer la fiabilité et l'efficacité de cette méthode avant de l'intégrer au bloc opératoire. / Prostate cancer is the most common cancer in men in France and western countries. It is the third leading cause of death from cancer, being responsible for around 10% of deaths. Brachytherapy, a radiotherapy technique, is associated with a better health-related quality of life after the treatment, compared to other treatment techniques. Prostate brachytherapy involves the implantation of radioactive sources inside the prostate to deliver a localized radiation dose to the tumor while sparing the surrounding healthy tissues. Multi-modal imaging is used in order to improve the overall accuracy of the treatment. The pre-operative Computed Tomography (CT) images can be used to calculate a personalized and accurate dose distribution. During the intervention, the surgeon utilizes a real-time guiding system, Trasnrectal Ultrasound (TRUS), to accurately place the radioactive sources in their desired pre-planned positions. Therefore, if the positions of the sources were determined on CT, they need to be transferred to US. However, a robust and direct US/CT registration is hardly possible since they both provide low soft tissue contrast. Magnetic Resonance Imaging (MRI), on the other hand, has a superior contrast and can potentially improve the treatment planning and delivery by providing a better visualization. Thus, these three modalities (MRI, US and CT) need to be accurately registered. To compensate for prostate deformations, caused by changes in size and form between the different acquisitions, non-rigid registration is essential. Fully automatic registration methodology is necessary in order to facilitate its integration in a clinical workflow. At first, we propose a registration between pre-operative MR and CT images based on the maximization of the mutual information in combination with a deformation field parameterized by cubic B-Splines. We propose to constrain the registration to volumes of interest (VOIs) in order to improve the robustness and the computational efficiency. The proposed approach was validated on clinical patient datasets. Quantitative evaluation indicated that the overall registration error was of 1.15±0.20 mm; which satisfies the desired clinical accuracy. Then, we propose a second intra-operative US/MRI registration, where a multi-resolution approach is implemented to reduce the probability of local minima and improve the computational efficiency. A similarity measure, which correlates intensities of the US image with intensities and gradient magnitude of the MRI, is used to determine the transformation that aligns the two images. The proposed methodology was validated on a prostate phantom at first to assess its feasibility. Subsequently, the method was validated on clinical patient datasets and evaluated using qualitative and quantitative criteria, resulting in a registration error of 1.44±0.06 mm. The approach proposed in this work allows going towards a multimodal protocol for image-guided brachytherapy which can improve the overall accuracy of this procedure. Despite such encouraging results, future work will involve further evaluation on a larger number of datasets in order to assess the reliability and the efficiency of this methodology before integrating it in a clinical workflow.

Le travail de thèse que nous présentons s’articule autour de l’utilisation de caméras motorisées à trois degrés de liberté, également appelées caméras PTZ. Ces caméras peuvent être pilotées suivant deux angles. L’angle de panorama (θ) permet une rotation autour d’un axe vertical et l’angle de tangage (ϕ) permet une rotation autour d’un axe horizontal. Si, théoriquement, ces caméras permettent donc une vue omnidirectionnelle, elles limitent le plus souvent la rotation suivant l’angle de panorama mais surtout suivant l’angle de tangage. En plus du pilotage des rotations, ces caméras permettent également de contrôler la distance focale permettant ainsi un degré de liberté supplémentaire. Par rapport à d’autres modèles, les caméras PTZ permettent de construire un panorama - représentation étendue d’une scène construite à partir d’une collection d’image - de très grande résolution. La première étape dans la construction d’un panorama est l’acquisition des différentes prises de vue. A cet effet, nous avons réalisé une étude théorique permettant une couverture optimale de la sphère à partir de surfaces rectangulaires en limitant les zones de recouvrement. Cette étude nous permet de calculer une trajectoire optimale de la caméra et de limiter le nombre de prises de vues nécessaires à la représentation de la scène. Nous proposons également différents traitements permettant d’améliorer sensiblement le rendu et de corriger la plupart des défauts liés à l’assemblage d’une collection d’images acquises avec des paramètres de prises de vue différents. Une part importante de notre travail a été consacrée au recalage automatique d’images en temps réel, c’est à dire que chaque étapes est effectuée en moins de 40ms pour permettre le traitement de 25 images par seconde. La technologie que nous avons développée permet d’obtenir un recalage particulièrement précis avec un temps d’exécution de l’ordre de 4ms (AMD1.8MHz). Enfin, nous proposons deux applications de suivi d’objets en mouvement directement issues de nos travaux de recherche. La première associe une caméra PTZ à un miroir sphérique. L’association de ces deux éléments permet de détecter tout objet en mouvement dans la scène puis de se focaliser sur l’un d’eux. Dans le cadre de cette application, nous proposons un algorithme de calibrage automatique de l’ensemble caméra et miroir. La deuxième application n’exploite que la caméra PTZ et permet la segmentation et le suivi des objets dans la scène pendant le mouvement de la caméra. Par rapport aux applications classiques de suivi de cible en mouvement avec une caméra PTZ, notre approche se différencie par le fait que réalisons une segmentation fine des objets permettant leur classification. / The thesis considers the of use motorized cameras with 3 degrees of freedom which are commonly called PTZ cameras. The orientation of such cameras is controlled according to two angles: the panorama angle (θ) describes the degree of rotation around on vertical axis and the tilt angle (ϕ) refers to rotation along a meridian line. Theoretically, these cameras can cover an omnidirectional field of vision of 4psr. Generally, the panorama angle and especially the tilt angle are limited for such cameras. In addition to control of the orientation of the camera, it is also possible to control focal distance, thus allowing an additional degree of freedom. Compared to other material, PTZ cameras thus allow one to build a panorama of very high resolution. A panorama is a wide representation of a scene built starting from a collection of images. The first stage in the construction of a panorama is the acquisition of the various images. To this end, we made a theoretical study to determine the optimal paving of the sphere with rectangular surfaces to minimize the number of zones of recovery. This study enables us to calculate an optimal trajectory of the camera and to limit the number of images necessary to the representation of the scene. We also propose various processing techniques which appreciably improve the rendering of the mosaic image and correct the majority of the defaults related to the assembly of a collection of images which were acquired with differing image capture parameters. A significant part of our work was used to the automatic image registration in real time, i.e. lower than 40ms. The technology that we developed makes it possible to obtain a particularly precise image registration with an computation time about 4ms (AMD1.8MHz). Our research leads directly to two proposed applications for the tracking of moving objects. The first involves the use of a PTZ camera and a spherical mirror. The combination of these two elements makes it possible to detect any motion object in the scene and to then to focus itself on one of them. Within the framework of this application, we propose an automatic algorithm of calibration of the system. The second application exploits only PTZ camera and allows the segmentation and the tracking of the objects in the scene during the movement of the camera. Compared to the traditional applications of motion detection with a PTZ camera, our approach is different by the fact that it compute a precise segmentation of the objects allowing their classification.

abstract: Multi-sensor fusion is a fundamental problem in Robot Perception. For a robot to operate in a real world environment, multiple sensors are often needed. Thus, fusing data from various sensors accurately is vital for robot perception. In the first part of this thesis, the problem of fusing information from a LIDAR, a color camera and a thermal camera to build RGB-Depth-Thermal (RGBDT) maps is investigated. An algorithm that solves a non-linear optimization problem to compute the relative pose between the cameras and the LIDAR is presented. The relative pose estimate is then used to find the color and thermal texture of each LIDAR point. Next, the various sources of error that can cause the mis-coloring of a LIDAR point after the cross- calibration are identified. Theoretical analyses of these errors reveal that the coloring errors due to noisy LIDAR points, errors in the estimation of the camera matrix, and errors in the estimation of translation between the sensors disappear with distance. But errors in the estimation of the rotation between the sensors causes the coloring error to increase with distance. On a robot (vehicle) with multiple sensors, sensor fusion algorithms allow us to represent the data in the vehicle frame. But data acquired temporally in the vehicle frame needs to be registered in a global frame to obtain a map of the environment. Mapping techniques involving the Iterative Closest Point (ICP) algorithm and the Normal Distributions Transform (NDT) assume that a good initial estimate of the transformation between the 3D scans is available. This restricts the ability to stitch maps that were acquired at different times. Mapping can become flexible if maps that were acquired temporally can be merged later. To this end, the second part of this thesis focuses on developing an automated algorithm that fuses two maps by finding a congruent set of five points forming a pyramid. Mapping has various application domains beyond Robot Navigation. The third part of this thesis considers a unique application domain where the surface displace- ments caused by an earthquake are to be recovered using pre- and post-earthquake LIDAR data. A technique to recover the 3D surface displacements is developed and the results are presented on real earthquake datasets: El Mayur Cucupa earthquake, Mexico, 2010 and Fukushima earthquake, Japan, 2011. / Dissertation/Thesis / Doctoral Dissertation Engineering Science 2016

Après une déprivation sensorielle ou après une réhabilitation sensorielle périphérique, les aires sensori-motrices primaires du cerveau se réorganisent anatomiquement et fonctionnellement. Dans le cas du transfert tendineux, une réhabilitation des fonctions manuelles est opérée grâce à une inversion de certaines fonctions de flexion en extension. Chez les patients opérés, la commande centrale de ces mouvements élémentaires repose sur des processus de plasticité cérébrale, processus encore mal connus, lents qui se stabilisent en une année et qui présentent une co-occurrence avec la récupération manuelle. Nous faisons l'hypothèse que l'IRM fonctionnelle de haute résolution permet de détecter la plasticité cérébrale liée à cette récupération motrice. Cette thèse a pour but de mettre en place des méthodes de suivi longitudinal individuel à partir des images fonctionnelles cérébrales des patients pour étudier la plasticité cérébrale lors de la récupération fonctionnelle. On a d’abord cherché à obtenir des cartes de référence de la motricité fine de la main sur un groupe de sujets contrôles. Ces cartes sont ensuite utilisées pour évaluer, à partir des données obtenues lors du suivi longitudinal de patients, la plasticité cérébrale liée au transfert tendineux. Pour mieux comprendre la représentation des mouvements de flexion et d'extension de la main dans le cortex moteur primaire, nous avons mis en place une étude en IRM fonctionnelle de haute résolution à 3T sur un groupe de 13 sujets sains. Pour généraliser les résultats individuels obtenus pour chaque mouvement au niveau de la population, il faut pouvoir réaligner les cerveaux individuels dans un référentiel commun afin d'effectuer une analyse statistique sur le groupe. Or, la variabilité anatomique inter-individuelle des aires motrices primaires constituait un verrou scientifique car celles-ci ne se réalignaient pas correctement par les méthodes classiques. Dans un premier temps, nous avons donc évalué différentes méthodes de recalage non-linéaires au niveau du cortex moteur pour assurer un alignement inter-individuel robuste. Nous avons comparé une méthode locale, Demons qui permet des déformations locales très importantes des images, une méthode classique non-linéaire (SPM), qui permet un alignement global des images, et une méthode de recalage global difféomorphique (DARTEL) utilisant de nombreux degrés de liberté. De plus, nous avons appliqué une méthode récente basée sur l’alignement des sillons corticaux au préalable à l’utilisation de DARTEL (DISCO+DARTEL) en partenariat avec l’équipe du LSIS, (CNRS Marseille) qui ajoute un caractère local à la technique globale de recalage. Nous montrons que cette dernière méthode produit le meilleur alignement sur des critères à la fois anatomiques (distance de Hausdorff, superposition des masques de tissus, et caractéristiques du champ de déformations) et fonctionnels (précision de la localisation et robustesse statistique des activations détectées). Nous avons alors pu établir des cartes de référence en haute résolution des mouvements élémentaires de la main, selon la dominance manuelle, selon la direction du mouvement et selon le segment de la main. Ces cartes présentent de multiples foyers d’activation et un chevauchement important dans la région dite du « hand-knob ». Dans un deuxième temps, nous avons évalué la robustesse de nos résultats, en réalisant une deuxième série d’examens sur les mêmes sujets contrôles (test-retest). Deux patients ont été suivis longitudinalement: avant la chirurgie (M0), à 1 mois (M1), à 3 (M3), 6 (M6) et 12 mois (M12) après la chirurgie. On a observé le recrutement au cours de la récupération de la SMA, de M1 et S1 ipsilatéral, de S1 contralatéral et des lobules V et VI du cervelet. Par rapport aux sujets sains, les patients mettent en place une réorganisation compensatoire au cours de la récupération fonctionnelle. / After a sensory deprivation or a peripheral sensory rehabilitation, primary sensorimotor areas undergo anatomical and functional reorganization. The hand tendon transfer is a rehabilitative surgery that restores the hand extension function by changing the insertion of chosen flexor muscles. During rehabilitation, the central control of the flexion and extension movements is based on elementary processes of brain plasticity, still poorly understood, but known to be slow, taking up to one year and occurring simultaneously with manual recovery. We hypothesize that high-resolution functional MRI (fMRI) may reveal brain plasticity linked to motor-behavior recovery.This PhD thesis aims to develop fMRI methods for individual patient follow-up after hand tendon transfer surgery. We first defined reference maps, based on a group of healthy subjects, for fine cortical representation of voluntary hand movements. These maps were then used to evaluate brain plasticity linked to the hand tendon surgery. To better understand the representation of the hand’s movements of flexion and extension in the primary motor cortex, we carried out a high-resolution, functional MRI study (using a static magnetic field of 3 Tesla), on a group of 13 healthy subjects. It was necessary to register all individual brains into a common reference system in order to perform a group statistical analysis. However, the inter-individual anatomical variability of the primary motor areas prevented us from performing the registration by conventional methods. We evaluated various methods of nonlinear registration to ensure a robust inter-individual alignment of central sulci. We compared: 1. a local method (Demon), which allows for important local deformations, 2. a standard non-linear method (SPM), which allows for a global image alignment and 3. a global diffeomorphic registration method (DARTEL) with a large number of degrees of freedom. In addition, we applied a fourth, more recent method, in partnership with LSIS, (CNRS Marseille) which iteratively reinforces the alignment of identified sulci before applying DARTEL (DISCO+DARTEL). This adds a local sulci-based constraint to the global deformation. We found that the fourth method produced the best alignment according to both anatomical criteria (Hausdorff distance, mask tissues overlaps and characteristics of the deformations field) and functional criteria (localization accuracy and statistical robustness of activations detected). We were then able to establish high spatial resolution reference maps of the elementary movements of the hand. These maps showed multiple foci of activity and significant overlaps in the region known as the "hand-knob."This first step of testing completed, we entered into a second round of testing where we evaluated the reproducibility of our initial results by performing a second series of tests on the same control group (“test-retest”).Two patients were followed up: before surgery (M0) and 1 month (M1), 3 (M3), 6 (M6) and 12 months (M12) after surgery. Functional recruitment was observed during recovery in SMA, M1, ispilateral and contralateral S1 and lobules V-VI of the cerebellum. Compared with healthy subjects, these two patients presented compensatory cortex reorganization during progressive recovery of hand function.