In the context of the female pelvic medicine, non-invasive magnetic resonance imaging is widely used for the diagnosis of pelvic floor disorders. Nowadays, in the clinical routine, diagnoses rely largely on human interpretation of medical images, on the experience of physicians, with sometimes subjective interpretations. Hence, image correlation methods would be an alternative way to assist physicians to provide more objective analyses with standard procedures and parametrisation for patient-specific cases. Moreover, the main symptoms of pelvic system pathologies are abnormal mobilities. The finite element model simulation is a powerful tool for understanding such mobilities. Both the patient-specific simulation and the image analysis require accurate and smooth geometries of the pelvic organs. This paper introduces a new method that can be classified as a model-to-image correlation approach. The method performs fast semi-automatic detection of the bladder, vagina and rectum from magnetic resonance images for geometries reconstruction and further study of the mobilities. The approach consists of fitting a B-spline model to the organ shapes in real images via a generated virtual image. We provided efficient, adaptive and consistent segmentation on a dataset of 19 patient images (healthy and pathological).

https://hal.inria.fr/hal-01204589/document

B-spline Based Multi-organ Detection in Magnetic Resonance Imaging

Segmenting structures of interest in medical images is an important step in different tasks such as visualization, quantitative analysis, simulation, and image-guided surgery, among several other clinical applications. Numerous segmentation methods have been developed in the past three decades for extraction of anatomical or functional structures on medical imaging. Deformable models, which include the active contour models or snakes, are among the most popular methods for image segmentation combining several desirable features such as inherent connectivity and smoothness. Even though different approaches have been proposed and significant work has been dedicated to the improvement of such algorithms, there are still challenging research directions as the simultaneous extraction of multiple objects and the integration of individual techniques. This paper presents a novel open-source framework called deformable model array (DMA) for the segmentation of multiple and complex structures of interest in different imaging modalities. While most active contour algorithms can extract one region at a time, DMA allows integrating several deformable models to deal with multiple segmentation scenarios. Moreover, it is possible to consider any existing explicit deformable model formulation and even to incorporate new active contour methods, allowing to select a suitable combination in different conditions. The framework also introduces a control module that coordinates the cooperative evolution of the snakes and is able to solve interaction issues toward the segmentation goal. Thus, DMA can implement complex object and multi-object segmentations in both 2D and 3D using the contextual information derived from the model interaction. These are important features for several medical image analysis tasks in which different but related objects need to be simultaneously extracted. Experimental results on both computed tomography and magnetic resonance imaging show that the proposed framework has a wide range of applications especially in the presence of adjacent structures of interest or under intra-structure inhomogeneities giving excellent quantitative results.

Multi-object segmentation framework using deformable models for medical imaging analysis.

A method is provided for generating a deformable model (300) for segmenting an anatomical structure in a medical image The anatomical structure comprises a wall The deformable model (300) is generated such that it comprises, in addition to two surface meshes (320, 360), an intermediate layer mesh (340) for being applied in-between a first surface layer of the wall and a second surface layer of the wall In generating the intermediate layer mesh (340), the mesh topology of at least part (400) of the intermediate layer mesh is matched to the mesh topology of one of the surface meshes (320, 360), thereby establishing matching mesh topologies The deformable model (300), as generated, better matches the composition of such walls, thereby providing a more accurate segmentation

Model-based segmentation of an anatomical structure

The aim of this work is to provide the surgeon-urologist with a system for automatic 2D and 3D-reconstruction of the bladder wall to help him within the treatment of bladder cancer as well as planning and documentation of the interventions. Within this small pilot-framework a fast feasibility study was made to clear if it is generally possible to build a bladder wall model using a special endoscope with an embedded laser-based distance measurement, an optical navigation system and modern image stitching techniques. Some experiments with a realistic bladder phantom have shown that this initial concept is generally acceptable and can be used with some extensions to build a system which can provide an automatic bladder wall reconstruction in real time to be used within a surgical intervention.

A high resolution bladder wall map: Feasibility study

The relatively limited understanding of the physiology of uterine activation prevents us from achieving optimal clinical outcomes for managing serious pregnancy disorders such as preterm birth or uterine dystocia. There is increasing awareness that multi-scale computational modeling of the uterus is a promising approach for providing a qualitative and quantitative description of uterine physiology. The overarching objective of such approach is to coalesce previously fragmentary information into a predictive and testable model of uterine activity that, in turn, informs the development of new diagnostic and therapeutic approaches to these pressing clinical problems. This article assesses current progress towards this goal. We summarize the electrophysiological basis of uterine activation as presently understood and review recent research approaches to uterine modeling at different scales from single cell to tissue, whole organ and organism with particular focus on transformative data in the last decade. We describe the positives and limitations of these approaches, thereby identifying key gaps in our knowledge on which to focus, in parallel, future computational and biological research efforts. 

/pdf/uterus-modeling-from-cell-to-organ-level-towards-better-nbn0lpdk.pdf

Uterus Modeling From Cell to Organ Level: Towards Better Understanding of Physiological Basis of Uterine Activity

The pelvic floor can be subjected to different disorders, coming from a physiological change in the spatial configuration of the organs of interest: the bladder, the rectum, the uterus and the vagina. However, resort to surgery to replace them is complicated to achieve. In order to support the decision of the surgeon as to the invasive method to use for the patient, the MoDyPe (Pelvis Dynamics Modeling) project was launched, aiming at building a patient specific pelvic organ behavior. Our approach consists in creating thick surfaces of hollow organs, using periodic B-splines and offsets, then in controlling their discretization and in exporting a hexahedral model to provide input data for the study on the dynamics of the soft bodies of interest. From a segmentation step providing a dataset of 3D points, a function is built to measure the bidirectional distance between the surface and the data. It is minimized with an alternate iterative Hoschek-like method, by updating the parametric map and moving the control points. Several offsets of the base surface are then created to build up the thickness of the organ.

Geometric modeling of pelvic organs

Physiological changes in the spatial configuration of the internal organs in the abdomen can induce different
disorders that need surgery. Following the complexity of the surgical procedure, mechanical simulations are
necessary but the in vivo factor makes complicate the study of pelvic organs. In order to determine a realistic
behavior of these organs, an accurate geometric model associated with a physical modeling is therefore required.
Our approach is integrated in the partnership between a geometric and physical module. The Geometric Modeling
seeks to build a continuous geometric model: from a dataset of 3D points provided by a Segmentation step,
surfaces are created through a B-spline fitting process. An energy function is built to measure the bidirectional
distance between surface and data. This energy is minimized with an alternate iterative Hoschek-like method. A
thickness is added with an offset formulation, and the geometric model is finally exported in a hexahedral mesh.
Afterward, the Physical Modeling tries to calculate the properties of the soft tissues to simulate the organs
displacements. The physical parameters attached to the data are determined with a feedback loop between
finite-elements deformations and ground-truth acquisition (dynamic MRI).

Geometric modeling of pelvic organs with thickness

In order to design a patient-specific simulator of pelvic organs, MoDyPe project considers the organs as thick surfaces. Starting from a closed parametric surface for the outer hull, an offset approach is applied. However, respecting the thickness on the surface and ensuring the absence of self-intersection is impossible if the shape has too important local curvatures. Two iterative approaches are compared. The first method is based on a B-spline formulation, and the second one on a mass-spring system (MSS). Our second method on discrete representation permits to obtain more accurate results with a more flexible formulation of the problem.

/pdf/geometric-modeling-of-pelvic-organs-with-a-discrete-offset-4oi0au5dvm.pdf

Geometric modeling of pelvic organs with a discrete offset approach

This paper deals with the construction of the Algebraic Trigonometric Pythagorean Hodograph (ATPH) cubic-like Hermite interpolant. A characterization of solutions according to the tangents at both ends and a global free shape parameter α is performed. Since this degree of freedom can be used for adjustments, we study how the curve evolves with respect to α. Several examples illustrating the construction process and a simple fitting method to determine the unique ATPH curve passing through a given point are proposed. 

/pdf/hermite-interpolation-by-planar-cubic-like-atph-3dr7xksy.pdf

Hermite interpolation by planar cubic-like ATPH

Modeling of soft pelvic organs and their thicknesses is a difficult task, especially when inputs are noisy and scattered. In order to define the geometric step for a global pelvic surgery simulator, we define a new method based only on geometry while considering the problem of error transfer between outer and inner organ surfaces. We compare this approach with a parametric formulation and a mass-spring system.

Discrete geometric modeling of thick pelvic organs with a medial axis

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