2,627 research outputs found

    3D Innovations in Personalized Surgery

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    Current practice involves the use of 3D surgical planning and patient-specific solutions in multiple surgical areas of expertise. Patient-specific solutions have been endorsed for several years in numerous publications due to their associated benefits around accuracy, safety, and predictability of surgical outcome. The basis of 3D surgical planning is the use of high-quality medical images (e.g., CT, MRI, or PET-scans). The translation from 3D digital planning toward surgical applications was developed hand in hand with a rise in 3D printing applications of multiple biocompatible materials. These technical aspects of medical care require engineers’ or technical physicians’ expertise for optimal safe and effective implementation in daily clinical routines.The aim and scope of this Special Issue is high-tech solutions in personalized surgery, based on 3D technology and, more specifically, bone-related surgery. Full-papers or highly innovative technical notes or (systematic) reviews that relate to innovative personalized surgery are invited. This can include optimization of imaging for 3D VSP, optimization of 3D VSP workflow and its translation toward the surgical procedure, or optimization of personalized implants or devices in relation to bone surgery

    Robust Estimation of Surface Curvature Information from Point Cloud Data

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    This paper surveys and evaluates some popular state of the art methods for algorithmic curvature and normal estimation. In addition to surveying existing methods we also propose a new method for robust curvature estimation and evaluate it against existing methods thus demonstrating its superiority to existing methods in the case of significant data noise. Throughout this paper we are concerned with computation in low dimensional spaces (N < 10) and primarily focus on the computation of the Weingarten map and quantities that may be derived from this; however, the algorithms discussed are theoretically applicable in any dimension. One thing that is common to all these methods is their basis in an estimated graph structure. For any of these methods to work the local geometry of the manifold must be exploited; however, in the case of point cloud data it is often difficult to discover a robust manifold structure underlying the data, even in simple cases, which can greatly influence the results of these algorithms. We hope that in pushing these algorithms to their limits we are able to discover, and perhaps resolve, many major pitfalls that may affect potential users and future researchers hoping to improve these methodsComment: 16 pages, 13 figure

    Interaction of elastomechanics and fluid dynamics in the human heart : Opportunities and challenges of light coupling strategies

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    Das menschliche Herz ist das hochkomplexe Herzstück des kardiovaskulären Systems, das permanent, zuverlässig und autonom den Blutfluss im Körper aufrechterhält. In Computermodellen wird die Funktionalität des Herzens nachgebildet, um Simulationsstudien durchzuführen, die tiefere Einblicke in die zugrundeliegenden Phänomene ermöglichen oder die Möglichkeit bieten, relevante Parameter unter vollständig kontrollierten Bedingungen zu variieren. Angesichts der Tatsache, dass Herz-Kreislauf-Erkrankungen die häufigste Todesursache in den Ländern der westlichen Hemisphäre sind, ist ein Beitrag zur frühzeit- igen Diagnose derselben von großer klinischer Bedeutung. In diesem Zusammenhang können computergestützte Strömungssimulationen wertvolle Einblicke in die Blutflussdynamik liefern und bieten somit die Möglichkeit, einen zentralen Bereich der Physik dieses multiphysikalischen Organs zu untersuchen. Da die Verformung der Endokardoberfläche den Blutfluss antreibt, müssen die Effekte der Elastomechanik als Randbedingungen für solche Strömungssimulationen berücksichtigt werden. Um im klinischen Kontext relevant zu sein, muss jedoch ein Mittelweg zwischen dem Rechenaufwand und der erforderlichen Genauigkeit gefunden werden, und die Modelle müssen sowohl robust als auch zuverlässig sein. Daher werden in dieser Arbeit die Möglichkeiten und Herausforderungen leichter und daher weniger komplexer Kopplungsstrategien mit Schwerpunkt auf drei Schlüsselaspekten bewertet: Erstens wird ein auf dem Immersed Boundary-Ansatz basierender Fluiddynamik-Löser implementiert, da diese Methode mit einer sehr robusten Darstellung von bewegten Netzen besticht. Die grundlegende Funktionalität wurde für verschiedene vereinfachte Geometrien verifiziert und zeigte eine hohe Übereinstimmung mit der jeweiligen analytischen Lösung. Vergleicht man die 3D-Simulation einer realistischen Geometrie des linken Teils des Herzens mit einem körperangepassten Netzbeschreibung, so wurden grundlegende globale Größen korrekt reproduziert. Allerdings zeigten Variationen der Randbedingungen einen großen Einfluss auf die Simulationsergebnisse. Die Anwendung des Lösers zur Simulation des Einflusses von Pathologien auf die Blutströmungsmuster ergab Ergebnisse in guter Übereinstimmung mit Literaturwerten. Bei Simulationen der Mitralklappeninsuffizienz wurde der rückströmende Anteil mit Hilfe einer Partikelverfolgungsmethode visualisiert. Bei hypertropher Kardiomyopathie wurden die Strömungsmuster im linken Ventrikel mit Hilfe eines passiven Skalartransports bewertet, um die lokale Konzentration des ursprünglichen Blutvolumens zu visualisieren. Da in den vorgenannten Studien nur ein unidirektionaler Informationsfluss vom elas- tomechanischen Modell zum Strömungslöser berücksichtigt wurde, wird die Rückwirkung des räumlich aufgelösten Druckfeldes aus den Strömungssimulationen auf die Elastomechanik quantifiziert. Es wird ein sequenzieller Kopplungsansatz eingeführt, um fluiddynamische Einflüsse in einer Schlag-für-Schlag-Kopplungsstruktur zu berücksichtigen. Die geringen Abweichungen im mechanischen Solver von 2 mm verschwanden bereits nach einer Iteration, was darauf schließen lässt, dass die Rückwirkungen der Fluiddynamik im gesunden Herzen begrenzt ist. Zusammenfassend lässt sich sagen, dass insbesondere bei Strömungsdynamiksimula- tionen die Randbedingungen mit Vorsicht gewählt werden müssen, da sie aufgrund ihres großen Einflusses die Anfälligkeit der Modelle erhöhen. Nichtsdestotrotz zeigten verein- fachte Kopplungsstrategien vielversprechende Ergebnisse bei der Reproduktion globaler fluiddynamischer Größen, während die Abhängigkeit zwischen den Lösern reduziert und Rechenaufwand eingespart wird

    Characterising the neck motor system of the blowfly

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    Flying insects use visual, mechanosensory, and proprioceptive information to control their movements, both when on the ground and when airborne. Exploiting visual information for motor control is significantly simplified if the eyes remain aligned with the external horizon. In fast flying insects, head rotations relative to the body enable gaze stabilisation during highspeed manoeuvres or externally caused attitude changes due to turbulent air. Previous behavioural studies into gaze stabilisation suffered from the dynamic properties of the supplying sensor systems and those of the neck motor system being convolved. Specifically, stabilisation of the head in Dipteran flies responding to induced thorax roll involves feed forward information from the mechanosensory halteres, as well as feedback information from the visual systems. To fully understand the functional design of the blowfly gaze stabilisation system as a whole, the neck motor system needs to be investigated independently. Through X-ray micro-computed tomography (ÎĽCT), high resolution 3D data has become available, and using staining techniques developed in collaboration with the Natural History Museum London, detailed anatomical data can be extracted. This resulted in a full 3- dimensional anatomical representation of the 21 neck muscle pairs and neighbouring cuticula structures which comprise the blowfly neck motor system. Currently, on the work presented in my PhD thesis, ÎĽCT data are being used to infer function from structure by creating a biomechanical model of the neck motor system. This effort aims to determine the specific function of each muscle individually, and is likely to inform the design of artificial gaze stabilisation systems. Any such design would incorporate both sensory and motor systems as well as the control architecture converting sensor signals into motor commands under the given physical constraints of the system as a whole.Open Acces

    Is beta in agreement with the relatives? Using relative clause sentences to investigate MEG beta power dynamics during sentence comprehension.

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    There remains some debate about whether beta power effects observed during sentence comprehension reflect ongoing syntactic unification operations (beta-syntax hypothesis), or instead reflect maintenance or updating of the sentence-level representation (beta-maintenance hypothesis). In this study, we used magnetoencephalography to investigate beta power neural dynamics while participants read relative clause sentences that were initially ambiguous between a subject- or an object-relative reading. An additional condition included a grammatical violation at the disambiguation point in the relative clause sentences. The beta-maintenance hypothesis predicts a decrease in beta power at the disambiguation point for unexpected (and less preferred) object-relative clause sentences and grammatical violations, as both signal a need to update the sentence-level representation. While the beta-syntax hypothesis also predicts a beta power decrease for grammatical violations due to a disruption of syntactic unification operations, it instead predicts an increase in beta power for the object-relative clause condition because syntactic unification at the point of disambiguation becomes more demanding. We observed decreased beta power for both the agreement violation and object-relative clause conditions in typical left hemisphere language regions, which provides compelling support for the beta-maintenance hypothesis. Mid-frontal theta power effects were also present for grammatical violations and object-relative clause sentences, suggesting that violations and unexpected sentence interpretations are registered as conflicts by the brain's domain-general error detection system.</p

    Riemannian statistical techniques with applications in fMRI

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    Over the past 30 years functional magnetic resonance imaging (fMRI) has become a fundamental tool in cognitive neuroimaging studies. In particular, the emergence of restingstate fMRI has gained popularity in determining biomarkers of mental health disorders (Woodward & Cascio, 2015). Resting-state fMRI can be analysed using the functional connectivity matrix, an object that encodes the temporal correlation of blood activity within the brain. Functional connectivity matrices are symmetric positive definite (SPD) matrices, but common analysis methods either reduce the functional connectivity matrices to summary statistics or fail to account for the positive definite criteria. However, through the lens of Riemannian geometry functional connectivity matrices have an intrinsic non-linear shape that respects the positive definite criteria (the affine-invariant geometry (Pennec, Fillard, & Ayache, 2006)). With methods from Riemannian geometric statistics, we can begin to explore the shape of the functional brain to understand this non-linear structure and reduce data-loss in our analyses. This thesis o↵ers two novel methodological developments to the field of Riemannian geometric statistics inspired by methods used in fMRI research. First we propose geometric- MDMR, a generalisation of multivariate distance matrix regression (MDMR) (McArdle & Anderson, 2001) to Riemannian manifolds. Our second development is Riemannian partial least squares (R-PLS), the generalisation of the predictive modelling technique partial least squares (PLS) (H. Wold, 1975) to Riemannian manifolds. R-PLS extends geodesic regression (Fletcher, 2013) to manifold-valued response and predictor variables, similar to how PLS extends multiple linear regression. We also generalise the NIPALS algorithm to Riemannian manifolds and suggest a tangent space approximation as a proposed method to fit R-PLS. In addition to our methodological developments, this thesis o↵ers three more contributions to the literature. Firstly, we develop a novel simulation procedure to simulate realistic functional connectivity matrices through a combination of bootstrapping and the Wishart distribution. Second, we propose the R2S statistic for measuring subspace similarity using the theory of principal angles between subspaces. Finally, we propose an extension of the VIP statistic from PLS (S. Wold, Johansson, & Cocchi, 1993) to describe the relationship between individual predictors and response variables when predicting a multivariate response with PLS. All methods in this thesis are applied to two fMRI datasets: the COBRE dataset relating to schizophrenia, and the ABIDE dataset relating to Autism Spectrum Disorder (ASD). We show that geometric-MDMR can detect group-based di↵erences between ASD and neurotypical controls (NTC), unlike its Euclidean counterparts. We also demonstrate the efficacy of R-PLS through the detection of functional connections related to schizophrenia and ASD. These results are encouraging for the role of Riemannian geometric statistics in the future of neuroscientific research.Thesis (Ph.D.) -- University of Adelaide, School of Mathematical Sciences, 202

    Geometric Data Analysis: Advancements of the Statistical Methodology and Applications

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    Data analysis has become fundamental to our society and comes in multiple facets and approaches. Nevertheless, in research and applications, the focus was primarily on data from Euclidean vector spaces. Consequently, the majority of methods that are applied today are not suited for more general data types. Driven by needs from fields like image processing, (medical) shape analysis, and network analysis, more and more attention has recently been given to data from non-Euclidean spaces–particularly (curved) manifolds. It has led to the field of geometric data analysis whose methods explicitly take the structure (for example, the topology and geometry) of the underlying space into account. This thesis contributes to the methodology of geometric data analysis by generalizing several fundamental notions from multivariate statistics to manifolds. We thereby focus on two different viewpoints. First, we use Riemannian structures to derive a novel regression scheme for general manifolds that relies on splines of generalized Bézier curves. It can accurately model non-geodesic relationships, for example, time-dependent trends with saturation effects or cyclic trends. Since Bézier curves can be evaluated with the constructive de Casteljau algorithm, working with data from manifolds of high dimensions (for example, a hundred thousand or more) is feasible. Relying on the regression, we further develop a hierarchical statistical model for an adequate analysis of longitudinal data in manifolds, and a method to control for confounding variables. We secondly focus on data that is not only manifold- but even Lie group-valued, which is frequently the case in applications. We can only achieve this by endowing the group with an affine connection structure that is generally not Riemannian. Utilizing it, we derive generalizations of several well-known dissimilarity measures between data distributions that can be used for various tasks, including hypothesis testing. Invariance under data translations is proven, and a connection to continuous distributions is given for one measure. A further central contribution of this thesis is that it shows use cases for all notions in real-world applications, particularly in problems from shape analysis in medical imaging and archaeology. We can replicate or further quantify several known findings for shape changes of the femur and the right hippocampus under osteoarthritis and Alzheimer's, respectively. Furthermore, in an archaeological application, we obtain new insights into the construction principles of ancient sundials. Last but not least, we use the geometric structure underlying human brain connectomes to predict cognitive scores. Utilizing a sample selection procedure, we obtain state-of-the-art results

    Numerical approach for the evaluation of hemodynamic behaviour in peripheral arterial disease : A systematic review

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    Reduced blood flow to the lower extremities causes peripheral arterial disease (PAD), which is caused by atherosclerotic plaque in the arterial wall. If this impairment is not treated, it will result in severe vascular diseases like ulceration and gangrene. Previous research has shown that while evaluating the pathology of the peripheral artery, the assumption of the model geometry significantly impacts the uncertainty of the stenosis area. However, more work needs to be done to understand the interaction between mechanical better and flow conditions in the peripheral artery using a separate computer model of the cardiovascular system. This paper reviews the numerical approach on pre and post-treatment of hemodynamic behavior in peripheral arterial disease (PAD). The goal of this study was to thoroughly examine the most recent developments with the application of computational studies in PAD from 2017 to 2022. While FSI investigation highlights the behavior of both the fluid and structure domains (blood and artery) during the numerical analysis of blood flow, CFD simulations primarily focus on the fluid domain (blood) behavior. Out of 92 research publications, 19 were appropriate for this assignment. This thorough study divides the publications into the categories of CFD, and FSI approaches. The results were then reviewed in accordance with the wall characteristic, analytical method, geometry, viscosity models, and validation. This paper summarizes the parameters of geometrical construction, viscosity models, analysis methods, and wall characteristics taken into consideration by the researchers to identify and simulate the blood flood flow in the stenosis area. These parameters are summarised in this study. Additionally, it could offer systematic data to help future studies produce better computational analyse

    3D Representation Learning for Shape Reconstruction and Understanding

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    The real world we are living in is inherently composed of multiple 3D objects. However, most of the existing works in computer vision traditionally either focus on images or videos where the 3D information inevitably gets lost due to the camera projection. Traditional methods typically rely on hand-crafted algorithms and features with many constraints and geometric priors to understand the real world. However, following the trend of deep learning, there has been an exponential growth in the number of research works based on deep neural networks to learn 3D representations for complex shapes and scenes, which lead to many cutting-edged applications in augmented reality (AR), virtual reality (VR) and robotics as one of the most important directions for computer vision and computer graphics. This thesis aims to build an intelligent system with dynamic 3D representations that can change over time to understand and recover the real world with semantic, instance and geometric information and eventually bridge the gap between the real world and the digital world. As the first step towards the challenges, this thesis explores both explicit representations and implicit representations by explicitly addressing the existing open problems in these areas. This thesis starts from neural implicit representation learning on 3D scene representation learning and understanding and moves to a parametric model based explicit 3D reconstruction method. Extensive experimentation over various benchmarks on various domains demonstrates the superiority of our method against previous state-of-the-art approaches, enabling many applications in the real world. Based on the proposed methods and current observations of open problems, this thesis finally presents a comprehensive conclusion with potential future research directions

    Surface-Based tools for Characterizing the Human Brain Cortical Morphology

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    Tesis por compendio de publicacionesThe cortex of the human brain is highly convoluted. These characteristic convolutions present advantages over lissencephalic brains. For instance, gyrification allows an expansion of cortical surface area without significantly increasing the cranial volume, thus facilitating the pass of the head through the birth channel. Studying the human brain’s cortical morphology and the processes leading to the cortical folds has been critical for an increased understanding of the pathological processes driving psychiatric disorders such as schizophrenia, bipolar disorders, autism, or major depression. Furthermore, charting the normal developmental changes in cortical morphology during adolescence or aging can be of great importance for detecting deviances that may be precursors for pathology. However, the exact mechanisms that push cortical folding remain largely unknown. The accurate characterization of the neurodevelopment processes is challenging. Multiple mechanisms co-occur at a molecular or cellular level and can only be studied through the analysis of ex-vivo samples, usually of animal models. Magnetic Resonance Imaging can partially fill the breach, allowing the portrayal of the macroscopic processes surfacing on in-vivo samples. Different metrics have been defined to measure cortical structure to describe the brain’s morphological changes and infer the associated microstructural events. Metrics such as cortical thickness, surface area, or cortical volume help establish a relation between the measured voxels on a magnetic resonance image and the underlying biological processes. However, the existing methods present limitations or room for improvement. Methods extracting the lines representing the gyral and sulcal morphology tend to over- or underestimate the total length. These lines can provide important information about how sulcal and gyral regions function differently due to their distinctive ontogenesis. Nevertheless, some methods label every small fold on the cortical surface as a sulcal fundus, thus losing the perspective of lines that travel through the deeper zones of a sulcal basin. On the other hand, some methods are too restrictive, labeling sulcal fundi only for a bunch of primary folds. To overcome this issue, we have proposed a Laplacian-collapse-based algorithm that can delineate the lines traversing the top regions of the gyri and the fundi of the sulci avoiding anastomotic sulci. For this, the cortex, represented as a 3D surface, is segmented into gyral and sulcal surfaces attending to the curvature and depth at every point of the mesh. Each resulting surface is spatially filtered, smoothing the boundaries. Then, a Laplacian-collapse-based algorithm is applied to obtain a thinned representation of the morphology of each structure. These thin curves are processed to detect where the extremities or endpoints lie. Finally, sulcal fundi and gyral crown lines are obtained by eroding the surfaces while preserving the structure topology and connectivity between the endpoints. The assessment of the presented algorithm showed that the labeled sulcal lines were close to the proposed ground truth length values while crossing through the deeper (and more curved) regions. The tool also obtained reproducibility scores better or similar to those of previous algorithms. A second limitation of the existing metrics concerns the measurement of sulcal width. This metric, understood as the physical distance between the points on opposite sulcal banks, can come in handy in detecting cortical flattening or complementing the information provided by cortical thickness, gyrification index, or such features. Nevertheless, existing methods only provided averaged measurements for different predefined sulcal regions, greatly restricting the possibilities of sulcal width and ignoring the intra-region variability. Regarding this, we developed a method that estimates the distance from each sulcal point in the cortex to its corresponding opposite, thus providing a per-vertex map of the physical sulcal distances. For this, the cortical surface is sampled at different depth levels, detecting the points where the sulcal banks change. The points corresponding to each sulcal wall are matched with the closest point on a different one. The distance between those points is the sulcal width. The algorithm was validated against a simulated sulcus that resembles a simple fold. Then the tool was used on a real dataset and compared against two widely-used sulcal width estimation methods, averaging the proposed algorithm’s values into the same region definition those reference tools use. The resulting values were similar for the proposed and the reference methods, thus demonstrating the algorithm’s accuracy. Finally, both algorithms were tested on a real aging population dataset to prove the methods’ potential in a use-case scenario. The main idea was to elucidate fine-grained morphological changes in the human cortex with aging by conducting three analyses: a comparison of the age-dependencies of cortical thickness in gyral and sulcal lines, an analysis of how the sulcal and gyral length changes with age, and a vertex-wise study of sulcal width and cortical thickness. These analyses showed a general flattening of the cortex with aging, with interesting findings such as a differential age-dependency of thickness thinning in the sulcal and gyral regions. By demonstrating that our method can detect this difference, our results can pave the way for future in vivo studies focusing on macro- and microscopic changes specific to gyri or sulci. Our method can generate new brain-based biomarkers specific to sulci and gyri, and these can be used on large samples to establish normative models to which patients can be compared. In parallel, the vertex-wise analyses show that sulcal width is very sensitive to changes during aging, independent of cortical thickness. This corroborates the concept of sulcal width as a metric that explains, in the least, the unique variance of morphology not fully captured by existing metrics. Our method allows for sulcal width vertex-wise analyses that were not possible previously, potentially changing our understanding of how changes in sulcal width shape cortical morphology. In conclusion, this thesis presents two new tools, open source and publicly available, for estimating cortical surface-based morphometrics. The methods have been validated and assessed against existing algorithms. They have also been tested on a real dataset, providing new, exciting insights into cortical morphology and showing their potential for defining innovative biomarkers.Programa de Doctorado en Ciencia y Tecnología Biomédica por la Universidad Carlos III de MadridPresidente: Juan Domingo Gispert López.- Secretario: Norberto Malpica González de Vega.- Vocal: Gemma Cristina Monté Rubi
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