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

Anatomy-Aware Inference of the 3D Standing Spine Posture from 2D Radiographs

An important factor for the development of spinal degeneration, pain and the outcome of spinal surgery is known to be the balance of the spine. It must be analyzed in an upright, standing position to ensure physiological loading conditions and visualize load-dependent deformations. Despite the complex 3D shape of the spine, this analysis is currently performed using 2D radiographs, as all frequently used 3D imaging techniques require the patient to be scanned in a prone position. To overcome this limitation, we propose a deep neural network to reconstruct the 3D spinal pose in an upright standing position, loaded naturally. Specifically, we propose a novel neural network architecture, which takes orthogonal 2D radiographs and infers the spine’s 3D posture using vertebral shape priors. In this work, we define vertebral shape priors using an atlas and a spine shape prior, incorporating both into our proposed network architecture. We validate our architecture on digitally reconstructed radiographs, achieving a 3D reconstruction Dice of 0.95, indicating an almost perfect 2D-to-3D domain translation. Validating the reconstruction accuracy of a 3D standing spine on real data is infeasible due to the lack of a valid ground truth. Hence, we design a novel experiment for this purpose, using an orientation invariant distance metric, to evaluate our model’s ability to synthesize full-3D, upright, and patient-specific spine models. We compare the synthesized spine shapes from clinical upright standing radiographs to the same patient’s 3D spinal posture in the prone position from CT

Generalizable Methods for Modeling Lumbar Spine Kinematics

A more complete understanding of lumbar spine kinematics could improve diagnoses and treatment of low back pathologies and may advance the development of biomechanical models. Kinematics describes motion of the five lumbar vertebrae without consideration for the forces that cause the motion. Despite considerable attention from researchers and clinicians, lumbar spine kinematics are not fully understood because the anatomy is not accessible for direct observation and the complex governing biomechanics produce small magnitude, coupled intervertebral movements. The overall goal of this project was to develop a descriptive model of intervertebral lumbar spine kinematics that is applicable to a generalizable subject population with diverse anthropometry. To accomplish this, a method was developed for measuring three-dimensional vertebral configuration using positional magnetic resonance imaging (MRI). The method makes use of automated vertebral registration to address time limitations in current data processing techniques and improves the ability to power experimental investigations. Finally, a geometric model of lumbar vertebral kinematics was developed using principal component regression applied to in vivo vertebral measurement data across the range of flexion and extension joint motion. This principal component-based approach offers unique advantages for predicting and interpreting performance of complex systems such as lumbar joint biomechanics because no assumptions are made regarding the governing mechanisms. This provides an opportunity to infer mechanistic characteristics about intervertebral joint kinematics and to use in vivo data to validate musculoskeletal models

A multi-center milestone study of clinical vertebral CT segmentation

A multiple center milestone study of clinical vertebra segmentation is presented in this paper. Vertebra segmentation is a fundamental step for spinal image analysis and intervention. The first half of the study was conducted in the spine segmentation challenge in 2014 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Workshop on Computational Spine Imaging (CSI 2014). The objective was to evaluate the performance of several state-of-the-art vertebra segmentation algorithms on computed tomography (CT) scans using ten training and five testing dataset, all healthy cases; the second half of the study was conducted after the challenge, where additional 5 abnormal cases are used for testing to evaluate the performance under abnormal cases. Dice coefficients and absolute surface distances were used as evaluation metrics. Segmentation of each vertebra as a single geometric unit, as well as separate segmentation of vertebra substructures, was evaluated. Five teams participated in the comparative study. The top performers in the study achieved Dice coefficient of 0.93 in the upper thoracic, 0.95 in the lower thoracic and 0.96 in the lumbar spine for healthy cases, and 0.88 in the upper thoracic, 0.89 in the lower thoracic and 0.92 in the lumbar spine for osteoporotic and fractured cases. The strengths and weaknesses of each method as well as future suggestion for improvement are discussed. This is the first multi-center comparative study for vertebra segmentation methods, which will provide an up-to-date performance milestone for the fast growing spinal image analysis and intervention

3D reconstruction for plastic surgery simulation based on statistical shape models

This thesis has been accomplished in Crisalix in collaboration with the Universitat Pompeu Fabra within the program of Doctorats Industrials. Crisalix has the mission of enhancing the communication between professionals of plastic surgery and patients by providing a solution to the most common question during the surgery planning process of ``How will I look after the surgery?''. The solution proposed by Crisalix is based in 3D imaging technology. This technology generates the 3D reconstruction that accurately represents the area of the patient that is going to be operated. This is followed by the possibility of creating multiple simulations of the plastic procedure, which results in the representation of the possible outcomes of the surgery. This thesis presents a framework capable to reconstruct 3D shapes of faces and breasts of plastic surgery patients from 2D images and 3D scans. The 3D reconstruction of an object is a challenging problem with many inherent ambiguities. Statistical model based methods are a powerful approach to overcome some of these ambiguities. We follow the intuition of maximizing the use of available prior information by introducing it into statistical model based methods to enhance their properties. First, we explore Active Shape Models (ASM) which are a well known method to perform 2D shapes alignment. However, it is challenging to maintain prior information (e.g. small set of given landmarks) unchanged once the statistical model constraints are applied. We propose a new weighted regularized projection into the parameter space which allows us to obtain shapes that at the same time fulfill the imposed shape constraints and are plausible according to the statistical model. Second, we extend this methodology to be applied to 3D Morphable Models (3DMM), which are a widespread method to perform 3D reconstruction. However, existing methods present some limitations. Some of them are based in non-linear optimizations computationally expensive that can get stuck in local minima. Another limitation is that not all the methods provide enough resolution to represent accurately the anatomy details needed for this application. Given the medical use of the application, the accuracy and robustness of the method, are important factors to take into consideration. We show how 3DMM initialization and 3DMM fitting can be improved using our weighted regularized projection. Finally, we present a framework capable to reconstruct 3D shapes of plastic surgery patients from two possible inputs: 2D images and 3D scans. Our method is used in different stages of the 3D reconstruction pipeline: shape alignment; 3DMM initialization and 3DMM fitting. The developed methods have been integrated in the production environment of Crisalix, proving their validity.Aquesta tesi ha estat realitzada a Crisalix amb la col·laboració de la Universitat Pompeu Fabra sota el pla de Doctorats Industrials. Crisalix té com a objectiu la millora de la comunicació entre els professionals de la cirurgia plàstica i els pacients, proporcionant una solució a la pregunta que sorgeix més freqüentment durant el procés de planificació d'una operació quirúrgica ``Com em veuré després de la cirurgia?''. La solució proposada per Crisalix està basada en la tecnologia d'imatge 3D. Aquesta tecnologia genera la reconstrucció 3D de la zona del pacient operada, seguit de la possibilitat de crear múltiples simulacions obtenint la representació dels possibles resultats de la cirurgia. Aquesta tesi presenta un sistema capaç de reconstruir cares i pits de pacients de cirurgia plàstica a partir de fotos 2D i escanegis. La reconstrucció en 3D d'un objecte és un problema complicat degut a la presència d'ambigüitats. Els mètodes basats en models estadístics son adequats per mitigar-les. En aquest treball, hem seguit la intuïció de maximitzar l'ús d'informació prèvia, introduint-la al model estadístic per millorar les seves propietats. En primer lloc, explorem els Active Shape Models (ASM) que són un conegut mètode fet servir per alinear contorns d'objectes 2D. No obstant, un cop aplicades les correccions de forma del model estadístic, es difícil de mantenir informació de la que es disposava a priori (per exemple, un petit conjunt de punts donat) inalterada. Proposem una nova projecció ponderada amb un terme de regularització, que permet obtenir formes que compleixen les restriccions de forma imposades i alhora són plausibles en concordança amb el model estadístic. En segon lloc, ampliem la metodologia per aplicar-la als anomenats 3D Morphable Models (3DMM) que són un mètode extensivament utilitzat per fer reconstrucció 3D. No obstant, els mètodes de 3DMM existents presenten algunes limitacions. Alguns estan basats en optimitzacions no lineals, computacionalment costoses i que poden quedar atrapades en mínims locals. Una altra limitació, és que no tots el mètodes proporcionen la resolució adequada per representar amb precisió els detalls de l'anatomia. Donat l'ús mèdic de l'aplicació, la precisió i la robustesa són factors molt importants a tenir en compte. Mostrem com la inicialització i l'ajustament de 3DMM poden ser millorats fent servir la projecció ponderada amb regularització proposada. Finalment, es presenta un sistema capaç de reconstruir models 3D de pacients de cirurgia plàstica a partir de dos possibles tipus de dades: imatges 2D i escaneigs en 3D. El nostre mètode es fa servir en diverses etapes del procés de reconstrucció: alineament de formes en imatge, la inicialització i l'ajustament de 3DMM. Els mètodes desenvolupats han estat integrats a l'entorn de producció de Crisalix provant la seva validesa

The computerization of archaeology: survey on AI techniques

This paper analyses the application of artificial intelligence techniques to various areas of archaeology and more specifically: a) The use of software tools as a creative stimulus for the organization of exhibitions; the use of humanoid robots and holographic displays as guides that interact and involve museum visitors; b) The analysis of methods for the classification of fragments found in archaeological excavations and for the reconstruction of ceramics, with the recomposition of the parts of text missing from historical documents and epigraphs; c) The cataloguing and study of human remains to understand the social and historical context of belonging with the demonstration of the effectiveness of the AI techniques used; d) The detection of particularly difficult terrestrial archaeological sites with the analysis of the architectures of the Artificial Neural Networks most suitable for solving the problems presented by the site; the design of a study for the exploration of marine archaeological sites, located at depths that cannot be reached by man, through the construction of a freely explorable 3D version

Virtuální rekonstrukce, její význam a přínos k paleobiologickému studiu fosilního člověka

Zachovalost kosterního materiálu je hlavní překážkou paleoantropologických studií. Virtuální metody se od 90. let 20. století staly důležitou součástí antropologického výzkumu, přičemž značně pomáhají překonat problémy zachovalosti, a to dvěma hlavními způsoby: zlepšují extrakci informací z fragmentárního materiálu a umožňují objektivnější rekonstrukci fragmentárních a nekompletních nálezů. Tato práce se zaměřila na virtuální rekonstrukci dvou fosilních nálezů: lebky moderního člověka Zlatý kůň (ZK; Česká republika) ze svrchního paleolitu a neandertálské pánve Regourdou 1 (R1) z Francie. Rekonstrukce lebky ZK nám umožnila revidovat pohlavní diagnózu a analyzovat její morfologickou afinitu. Na základě sekundární pohlavní diagnózy byl jedinec ZK s vysokou pravděpodobností žena a lebka vykazuje afinitu k rané svrchně paleolitické populaci. Pánev R1 vykazuje značnou asymetrii, která byla nejprve analyzována na křížové kosti v porovnání se zdravými moderními lidmi a neandertálci. Asymetrie výrazně překračuje variabilitu pozorovanou v současné populaci a mohla souviset s asymetrickým přenosem zátěže. Výrazná asymetrie byla proto zohledněna při následné rekonstrukci pánve, která nám umožnila posoudit pohlaví jedince a analyzovat transverzální rozměry pánevního kanálu a orientaci křížové kosti. Na základě...Preservation is a major obstacle in paleoanthropological studies. Since 1990s virtual methods have become an important part of anthropological research helping to overcome preservation problems in two principle ways: they improve extraction of information from a fragmentary material, and they permit a more objective reconstruction of fragmentary and incomplete remains. This thesis has focused on the virtual reconstruction of two fossil specimens: the modern human cranium from the Upper Paleolithic site of Zlatý kůň (ZK; Czech Republic) and the Neandertal Regourdou 1 (R1) pelvis (France). The reconstruction of the ZK cranium allowed us to revise sex attribution and analyze morphological affinity. Based on the secondary sex diagnosis, the ZK individual was most probably a female and exhibits a great affinity to Early Upper Paleolithic population. The R1 pelvis shows considerable asymmetry that was first analyzed on the sacrum in comparison with healthy modern humans and Neandertals. The asymmetry exceeds normal variation observed in the extant population and could have related to asymmetrical load dissipation. Therefore, the asymmetry was considered in the subsequent preliminary pelvic reconstruction which allowed us to assess sex of the individual and to analyze transverse dimensions of the pelvic...Katedra antropologie a genetiky člověkaDepartment of Anthropology and Human GeneticsPřírodovědecká fakultaFaculty of Scienc

Design and development of a multiscale model for the osteoporotic fracture prevention: a preclinical tool

Se espera que la osteoporosis sea partícipe de más de 9 millones de nuevas fracturas en todo el mundo en un futuro no muy lejano, ya que es una de las enfermedades con mayor índice de impacto entre la población de los países desarrollados. Se define como una enfermedad sistémica caracterizada por la pérdida de masa ósea y una alteración de su microestructura interna con la consiguiente susceptibilidad a la fractura. Actualmente, la estimación del riesgo de fractura se lleva a cabo mediante tomografía axial computerizada (TAC), Rayos X o densitometrías. Sin embargo, las simulaciones por elementos finitos para un paciente determinado, pueden contener una gran cantidad de información que permitirían unas predicciones más precisas. Una metodología multiescala ayudaría al desarrollo y caracterización de modelos de fractura más robustos que permitirían conocer de una manera más detallada el comportamiento del hueso. Además, dichos modelos podrían incorporar parámetros relacionados con la edad, el grado de osteoporosis o el tratamiento mediante fármacos. De hecho, debido a que el hueso trabecular interviene, en gran medida, en las fracturas de cadera osteoporóticas, un tratamiento preventivo alternativo para reducir el riesgo de fractura osteoporótica consistiría en la inyección de cemento óseo (PMMA) en el fémur osteoporótico.Por lo tanto, el principal objetivo de esta tesis doctoral es el desarrollo de un modelo multiescala para la prevención de la fractura ósea osteoporótica. Este modelo nos permitirá conocer más acerca de los mecanismos de fallo asociados a la osteoporosis desde el nivel tisular hasta el nivel macroscópico a fin de evaluar la factibilidad de la femoroplastia. Para alcanzar este objetivo, en primer lugar, se ha llevado a cabo una caracterización in vitro e in silico de estructuras artificiales de hueso artificial, denominadas open-cell (Sawbones, Malmö, Sweden), con propiedades próximas al hueso sano y osteoporótico, de manera que permita elucidar mecanismos de fractura asociados a la osteoporosis desde el nivel tisular. De esta manera, se han empleado métodos experimentales y computacionales basados en el procesado de imagen con el fin de estimar el módulo elástico y las porosidades de las diferentes estructuras open-cell. Las resultados computacionales y experimentales fueron comparados con los datos aportados por el fabricante. Se apreciaron importantes diferencias no sólo en términos del módulo de Young sino también en las porosidades. Posteriormente, se desarrolló un modelo discreto de partículas basado en la Teoría del Movimiento Aleatorio para simular la infiltración de cemento a través de las estructuras open-cell, previamente caracterizadas. Los parámetros del modelo incluyeron no sólo la viscosidad del cemento (alta o baja) sino la dirección de inyección (vertical o diagonal). De nuevo, se llevó a cabo una caracterización in vitro e in silico de las estructuras cementadas, validando el modelo computacional mediante ensayos experimentales. Dichos resultados mostraron que el modelo discreto de partículas era suficientemente robusto para su aplicación en la escala macroscópica. También, se inyectó cemento in vivo en fémures de conejo a fin de evaluar la factibilidad de la femoroplastia. Finalmente, se utilizaron fémures sanos y osteoporóticos para la predicción computacional del grado de mejora de las propiedades mecánicas cuando se inyectaba cemento de alta o baja viscosidad. El cemento de baja viscosidad mejoraba notablemente las cargas de fractura con respecto a los fémures no cementados. Los resultados finales mostraron que el cemento óseo mejora definitivamente las propiedades del hueso osteoporótico y la metodología propuesta puede llegar a utilizarse como una herramienta preclínica para un diagnóstico más preciso.<br /