3D reconstruction of ribcage geometry from biplanar radiographs using a statistical parametric model approach

Rib cage 3D reconstruction is an important prerequisite for thoracic spine modelling, particularly for studies of the deformed thorax in adolescent idiopathic scoliosis. This study proposes a new method for rib cage 3D reconstruction from biplanar radiographs, using a statistical parametric model approach. Simplified parametric models were defined at the hierarchical levels of rib cage surface, rib midline and rib surface, and applied on a database of 86 trunks. The resulting parameter database served to statistical models learning which were used to quickly provide a first estimate of the reconstruction from identifications on both radiographs. This solution was then refined by manual adjustments in order to improve the matching between model and image. Accuracy was assessed by comparison with 29 rib cages from CT scans in terms of geometrical parameter differences and in terms of line-to-line error distance between the rib midlines. Intra and inter-observer reproducibility were determined regarding 20 scoliotic patients. The first estimate (mean reconstruction time of 2’30) was sufficient to extract the main rib cage global parameters with a 95% confidence interval lower than 7%, 8%, 2% and 4° for rib cage volume, antero-posterior and lateral maximal diameters and maximal rib hump, respectively. The mean error distance was 5.4 mm (max 35mm) down to 3.6 mm (max 24 mm) after the manual adjustment step (+3’30). The proposed method will improve developments of rib cage finite element modeling and evaluation of clinical outcomes.This work was funded by Paris Tech BiomecAM chair on subject specific muscular skeletal modeling, and we express our acknowledgments to the chair founders: Cotrel foundation, Société générale, Protéor Company and COVEA consortium. We extend your acknowledgements to Alina Badina for medical imaging data, Alexandre Journé for his advices, and Thomas Joubert for his technical support

From Fully-Supervised, Single-Task to Scarcely-Supervised, Multi-Task Deep Learning for Medical Image Analysis

Image analysis based on machine learning has gained prominence with the advent of deep learning, particularly in medical imaging. To be effective in addressing challenging image analysis tasks, however, conventional deep neural networks require large corpora of annotated training data, which are unfortunately scarce in the medical domain, thus often rendering fully-supervised learning strategies ineffective.This thesis devises for use in a variety of medical image analysis applications a series of novel deep learning methods, ranging from fully-supervised, single-task learning to scarcely-supervised, multi-task learning that makes efficient use of annotated training data. Specifically, its main contributions include (1) fully-supervised, single-task learning for the segmentation of pulmonary lobes from chest CT scans and the analysis of scoliosis from spine X-ray images; (2) supervised, single-task, domain-generalized pulmonary segmentation in chest X-ray images and retinal vasculature segmentation in fundoscopic images; (3) largely-unsupervised, multiple-task learning via deep generative modeling for the joint synthesis and classification of medical image data; and (4) partly-supervised, multiple-task learning for the combined segmentation and classification of chest and spine X-ray images

Analyse de la géométrie externe du tronc scoliotique en flexion latérale

Scoliose idopathique -- Topographie de surface du tronc scoliotique -- Indices calculés à partir de la géométrie externe du tronc -- Calcul des courbes géodésiques sur un maillage 3D -- Objectifs du projet -- Protocole d'acquisition de données 3D -- Méthode d'extraction de sections selon la vallée du dos -- Méthodes d'évaluation -- Évaluation qualitative de la méthode d'extraction des sections à partir de la vallée du dos -- Évaluation des asymétries externes et des corrections prostopératoires obtenues avec les deux types de sections extraites sur des troncs scoliotiques -- Évaluation des tests de flexion latérale -- Protocole d'acquisition des données lors des tests de flexion latérale et reconstruction 3D du tronc en posture de flexion -- Extraction des sections selon la méthode proposée -- Analyse des asymétries externes du tronc -- Effet des tests de flexion latérale sur la géométrie externe du tronc

Medical Image Registration Using Deep Neural Networks

Registration is a fundamental problem in medical image analysis wherein images are transformed spatially to align corresponding anatomical structures in each image. Recently, the development of learning-based methods, which exploit deep neural networks and can outperform classical iterative methods, has received considerable interest from the research community. This interest is due in part to the substantially reduced computational requirements that learning-based methods have during inference, which makes them particularly well-suited to real-time registration applications. Despite these successes, learning-based methods can perform poorly when applied to images from different modalities where intensity characteristics can vary greatly, such as in magnetic resonance and ultrasound imaging. Moreover, registration performance is often demonstrated on well-curated datasets, closely matching the distribution of the training data. This makes it difficult to determine whether demonstrated performance accurately represents the generalization and robustness required for clinical use. This thesis presents learning-based methods which address the aforementioned difficulties by utilizing intuitive point-set-based representations, user interaction and meta-learning-based training strategies. Primarily, this is demonstrated with a focus on the non-rigid registration of 3D magnetic resonance imaging to sparse 2D transrectal ultrasound images to assist in the delivery of targeted prostate biopsies. While conventional systematic prostate biopsy methods can require many samples to be taken to confidently produce a diagnosis, tumor-targeted approaches have shown improved patient, diagnostic, and disease management outcomes with fewer samples. However, the available intraoperative transrectal ultrasound imaging alone is insufficient for accurate targeted guidance. As such, this exemplar application is used to illustrate the effectiveness of sparse, interactively-acquired ultrasound imaging for real-time, interventional registration. The presented methods are found to improve registration accuracy, relative to state-of-the-art, with substantially lower computation time and require a fraction of the data at inference. As a result, these methods are particularly attractive given their potential for real-time registration in interventional applications

Sensores em fibra ótica para o estudo biomecânico do disco intervertebral

Doutoramento em Engenharia MecânicaO presente trabalho teve como objetivo principal estudar o comportamento mecânico do disco intervertebral recorrendo a sensores em fibra ótica. Na expetativa de efetuar o melhor enquadramento do tema foi efetuada uma revisão exaustiva das várias configurações de sensores em fibra ótica que têm vindo a ser utilizadas em aplicações biomédicas e biomecânicas, nomeadamente para medição de temperatura, deformação, força e pressão. Nesse âmbito, procurou-se destacar as potencialidades dos sensores em fibra ótica e apresentá-los como uma tecnologia alternativa ou até de substituição das tecnologias associadas a sensores convencionais. Tendo em vista a aplicação de sensores em fibra ótica no estudo do comportamento do disco intervertebral efetuou-se também uma revisão exaustiva da coluna vertebral e, particularmente, do conceito de unidade funcional. A par de uma descrição anatómica e funcional centrada no disco intervertebral, vértebras adjacentes e ligamentos espinais foram ainda destacadas as suas propriedades mecânicas e descritos os procedimentos mais usuais no estudo dessas propriedades. A componente experimental do presente trabalho descreve um conjunto de experiências efetuadas com unidades funcionais cadavéricas utilizando sensores convencionais e sensores em fibra ótica com vista à medição da deformação do disco intervertebral sob cargas compressivas uniaxiais. Inclui ainda a medição in vivo da pressão intradiscal num disco lombar de uma ovelha sob efeito de anestesia. Para esse efeito utilizou-se um sensor comercial em fibra ótica e desenvolveu-se a respetiva unidade de interrogação. Finalmente apresenta-se os resultados da investigação em curso que tem como objetivo propor e desenvolver protótipos de sensores em fibra ótica para aplicações biomédicas e biomecânicas. Nesse sentido, são apresentadas duas soluções de sensores interferométricos para medição da pressão em fluídos corporais.The present work aimed to study the mechanical behavior of the intervertebral disc using fiber optic sensors. To address the theme an exhaustive review of the various configurations of fiber optic sensors that have been used in biomechanical and biomedical applications, in particular for measuring temperature, strain, force and pressure, was conducted. In this context, an effort was made to highlight the advantages of fiber optic sensors and present them as an alternative or even a substitution technology to conventional sensors. In view of the application of fiber optic sensors to study intervertebral disc behavior an exhaustive review of the spine and, particularly, of the spinal motion segment was made. Along with an anatomical and functional description of the intervertebral disc, the adjacent vertebrae and spinal ligaments, their mechanical properties were also highlighted as well as the most common procedures and guidelines followed in the study of these properties. The experimental section of the present work describes a set of tests performed with cadaveric spinal motion segments using conventional and fiber optic sensors to assess strain of the intervertebral disc under uniaxial compressive loads. This section also includes an experience reporting in vivo pressures measured in the lumbar disc of a sheep under general anesthesia. In this case, a commercial fiber optic sensor and a purpose-built interrogation unit were used. Finally, the results of ongoing research aiming to develop fiber optic sensors prototypes for biomedical and biomechanical applications are presented. Thus, the proof of concept of two possible interferometric configurations intended for pressure measurement in body fluids was presented

The effect of prefabricated wrist-hand orthoses on performing activities of daily living

Wrist-hand orthoses (WHOs) are commonly prescribed to manage the functional deficit associated with the wrist as a result of rheumatoid changes. The common presentation of the wrist is one of flexion and radial deviation with ulnar deviation of the fingers. This wrist position Results in altered biomechanics compromising hand function during activities of daily living (ADL). A paucity of evidence exists which suggests that improvements in ADL with WHO use are very task specific. Using normal subjects, and thus in the absence of pain as a limiting factor, the impact of ten WHOs on performing five ADLs tasks was investigated. The tasks were selected to represent common grip patterns and tests were performed with and without WHOs by right-handed, females, aged 20-50 years over a ten week period. The time taken to complete each task was recorded and a wrist goniometer, elbow goniometer and a forearm torsiometer were used to measure joint motion. Results show that, although orthoses may restrict the motion required to perform a task, participants do not use the full range of motion which the orthoses permit. The altered wrist position measured may be attributable to a modified method of performing the task or to a necessary change in grip pattern, resulting in an increased time in task performance. The effect of WHO use on ADL is task specific and may initially impede function. This could have an effect on WHO compliance if there appears to be no immediate benefits. This orthotic effect may be related to restriction of wrist motion or an inability to achieve the necessary grip patterns due to the designs of the orthoses