Browsing by Author "Bourgeat, P"

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    3D shape context surface registration for cortical mapping
    (Institute of Electrical and Electronics Engineers (IEEE), 2010-04-16) Acosta, O; Fripp, J; Rueda, A; Xiao, D; Bonner, E; Bourgeat, P; Salvado, O
    Deformable registration of cortical surfaces facilitates longitudinal and intergroup comparisons of cortical structure and function in the study of many neurodegenerative diseases. Non-rigid cortical matching is a challenging task due to the large variability between individuals and the complexity of the cortex. We present a new framework for computing cortical correspondences on brain surfaces based on 3D Shape Context and mean curvatures of partially flattened surfaces (PFS). Our approach is scale invariant and provides an accurate and anatomically meaningful alignment across the population. Registering PFS, instead of original cortical surfaces, simplifies the determination of shape correspondences, overcoming the problem of intersubject variability, while still guaranteeing the alignment of the main brain lobes and folding patterns. We validated the approach using 30 segmented brains from the OASIS database registered to a common space and compared the results with Freesurfer. In average, mean absolute distance of 0.36 and Hausdorff distance of 5.06 between moving and target surfaces are obtained. Further localization of labelled areas on each hemisphere demonstrated the accuracy of the technique.
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    Hybrid non-rigid registration method for registering rat skeletons from micro-CT images
    (Society of Nuclear Medicine and Molecular Imaging, 2009-05) Xiao, D; Zahra, D; Bourgeat, P; Tamayo, OA; Berghofer, PJ; Fripp, J; Grégoire, MC; Salvado, O
    Objectives: A hybrid non-rigid registration method for automatic rat spine detection and registration and further rat limbs registration was proposed. Methods: We first developed an automatic algorithm to extract the rat spine from its whole-body skeleton and then detect top point on the spinous process of each vertebra starting from the first vertebra at thoracic vertebrae towards the tail. The extracted points were matched to the predefined corresponding points of the spine in a rat atlas. Their correspondences field was used to perform skeletons registration by thin-plate-spline (TPS). Further, we extend 3D shape context algorithm for landmarks matching for rat limbs between the atlas and the newly extracted skeletons. The correspondences found were used to perform the rat limb skeletons registration by TPS. Results: Experiments were described using phantoms and actual rat skeletons. Mean square errors decrease was observed during registration process. Visually, the skeletons were successfully registered. Conclusions: The method can improve the robustness of rat skeleton registration, even in the case of large variation in some postures and this first step work can be extended to further improve rat organs registration guided by the correspondences found from the skeletons.© 2009 by Society of Nuclear Medicine
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    An improved 3D shape context based non-rigid registration method and its application to small animal skeletons registration
    (Pergamon-Elsevier Science Ltd, 2010-06-01) Xiao, D; Zahra, D; Bourgeat, P; Berghofer, PJ; Tamayo, OA; Wimberley, CA; Grégoire, MC; Salvado, O
    3D shape context is a method to define matching points between similar shapes. It can be used as a preprocessing step in a non-rigid registration. The main limitation of the method is point mismatching, which includes long geodesic distance mismatch causing wrong topological structure, and neighbors crossing mismatch between two adjacent points. In this paper, we propose a topological structure verification method to correct the long geodesic distance mismatch and a correspondence field smoothing method to correct the neighbors crossing mismatch. A robust 3D shape context model is generated and further combined with thin-plate spline model for non-rigid registration. The method was tested on phantoms and applied to rat hind limb and mouse hind limb skeletons registration from micro-CT images. Errors between the registered surfaces were reduced by using the proposed method. The robustness of the method is demonstrated. © 2010, Elsevier Ltd.
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    An improved 3D shape context registration method for non-rigid surface registration.
    (Society of Photo-optical Instrumentation Engineers (SPIE), 2010-02-14) Xiao, D; Zahra, D; Bourgeat, P; Berghofer, PJ; Tamayo, AO; Wimberley, CA; Grégoire, MC; Salvado, O
    3D shape context is a method to define matching points between similar shapes as a pre-processing step to non-rigid registration. The main limitation of the approach is point mismatching, which includes long geodesic distance mismatch and neighbors crossing mismatch. In this paper, we propose a topological structure verification method to correct the long geodesic distance mismatch and a correspondence field smoothing method to correct the neighbors crossing mismatch. A robust 3D shape context model is proposed and further combined with thin-plate spline model for non-rigid surface registration. The method was tested on phantoms and rat hind limb skeletons from micro CT images. The results from experiments on mouse hind limb skeletons indicate that the approach is robust.
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    Non-rigid registration method for mouse whole body skeleton registration.
    (Society of Photo-optical Instrumentation Engineers (SPIE), 2010-02-14) Xiao, D; Zahra, D; Bourgeat, P; Berghofer, PJ; Tamayo, AO; Wimberley, CA; Grégoire, MC; Salvado, O
    Micro-CT/PET imaging scanner provides a powerful tool to study tumor in small rodents in response to therapy. Accurate image registration is a necessary step to quantify the characteristics of images acquired in longitudinal studies. Small animal registration is challenging because of the very deformable body of the animal often resulting in different postures despite physical restraints. In this paper, we propose a non-rigid registration approach for the automatic registration of mouse whole body skeletons, which is based on our improved 3D shape context non-rigid registration method. The whole body skeleton registration approach has been tested on 21 pairs of mouse CT images with variations of individuals and time-instances. The experimental results demonstrated the stability and accuracy of the proposed method for automatic mouse whole body skeleton registration. © 2012, SPIE.