Jose Pozo - Academia.edu (original) (raw)

Papers by Jose Pozo

J. Open Source Softw., 2021

By definition, prehistorical societies are characterized by the absence of a writing system. Duri... more By definition, prehistorical societies are characterized by the absence of a writing system. During, the largest part of human history, and everywhere in the world, symbolic expressions belong mostly to illiterate societies which express themselves with rock-art paintings, pottery decorations, figurines, statuary, etc., and a lot of now disappeared carved woods, textile design, etc. These graphical expressions are the most significant remaining part of humankind’s symbolism. At the composition level, the presence of recurrent patterns of signs (i.e., graphical syntax) in meaningful associations indicates the existence of social conventions in the way to display and to read these expressions. Well-established and shared methods to record and study these graphical contents would open the possibility of cross-cultural comparisons at a large scale and over the long-term.

This paper introduces some general properties of the gravitational metric and the natural basis o... more This paper introduces some general properties of the gravitational metric and the natural basis of vectors and covectors in 4-dimensional emission coordinates. Emission coordinates are a class of space-time coordinates defined and generated by 4 emitters (satellites) broadcasting their proper time by means of electromagnetic signals. They are a constitutive ingredient of the simplest conceivable relativistic positioning systems. Their study is aimed to develop a theory of these positioning systems, based on the framework and concepts of general relativity, as opposed to introducing `relativistic effects' in a classical framework. In particular, we characterize the causal character of the coordinate vectors, covectors and 2-planes, which are of an unusual type. We obtain the inequality conditions for the contravariant metric to be Lorentzian, and the non-trivial and unexpected identities satisfied by the angles formed by each pair of natural vectors. We also prove that the metric...

Two essential properties of energy-momentum tensors T_μν are their positivity and conservation. T... more Two essential properties of energy-momentum tensors T_μν are their positivity and conservation. This is mathematically formalized by, respectively, an energy condition, as the dominant energy condition, and the vanishing of their divergence ∇^μ T_μν=0. The classical Bel and Bel-Robinson superenergy tensors, generated from the Riemann and Weyl tensors, respectively, are rank-4 tensors. But they share these two properties with energy momentum tensors: the Dominant Property (DP) and the divergence-free property in the absence of sources (vacuum). Senovilla defined a universal algebraic construction which generates a basic superenergy tensor TA from any arbitrary tensor A. In this construction the seed tensor A is structured as an r-fold multivector, which can always be done. The most important feature of the basic superenergy tensors is that they satisfy automatically the DP, independently of the generating tensor A. In a previous paper we presented a more compact definition of TA usin...

The MIDAS Journal, 2008

An algorithm for minimally interactive coronary artery tracking is presented. Tracking ability an... more An algorithm for minimally interactive coronary artery tracking is presented. Tracking ability and accuracy results are demonstrated on 16 images CTA images. First, a region of interest is automatically selected and a denoising filter applied. Then, for each voxel the probability of belonging to a coronary vessel is estimated from a feature space and a vesselness measure is used to obtain a cost function. The vessel starting point is obtained automatically, while the end point is provided by the user. Finally, the centerline is obtained as the minimal cost path between both points.

Two essential properties of energy–momentum tensors Tμν are their positivity and conservation. Th... more Two essential properties of energy–momentum tensors Tμν are their positivity and conservation. This is mathematically formalized by, respectively, an energy condition, as the dominant energy condition, and the vanishing of their divergence ∇Tμν = 0. The classical Bel and Bel-Robinson superenergy tensors, generated from the Riemann and Weyl tensors, respectively, are rank-4 tensors. But they share these two properties with energy–momentum tensors: the dominant property (DP) and the divergence-free property in the absence of sources (vacuum). Senovilla [2, 3] defined a universal algebraic construction which generates a basic superenergy tensor T {A} from any arbitrary tensor A. In this construction, the seed tensor A is structured as an r-fold multivector, which can always be done. The most important feature of the basic superenergy tensors is that they satisfy automatically the DP, independently of the generating tensor A. In [8], we presented a more compact definition of T {A} using...

Abstract. This paper introduces some general properties of the gravitational metric and the natur... more Abstract. This paper introduces some general properties of the gravitational metric and the natural basis of vectors and covectors in 4-dimensional emission coordinates. Emission coordinates are a class of space-time coordinates defined and generated by 4 emitters (satellites) broadcasting their proper time by means of electromagnetic signals. They are a constitutive ingredient of the simplest conceivable relativistic positioning systems. Their study is aimed to develop a theory of these positioning systems, based on the framework and concepts of general relativity, as opposed to introducing ‘relativistic effects’ in a classical framework. In particular, we characterize the causal character of the coordinate vectors, covectors and 2-planes, which are of an unusual type. We obtain the inequality conditions for the contravariant metric to be Lorentzian, and the non-trivial and unexpected identities satisfied by the angles formed by each pair of natural vectors. We also prove that the ...

IEEE Transactions on Medical Imaging, 2019

Osteoporosis is an age-associated disease characterised by low bone mineral density (BMD) and mic... more Osteoporosis is an age-associated disease characterised by low bone mineral density (BMD) and microarchitectural deterioration leading to enhanced fracture risk. Conventional dual-energy X-ray absorptiometry (DXA) analysis has facilitated our understanding of BMD reduction in specific regions of interest (ROIs) within the femur, but cannot resolve spatial BMD patterns nor reflect age-related changes in bone microarchitecture due to its inherent averaging of pixel BMD values into large ROIs. To address these limitations and develop a comprehensive model of involutional bone loss, this paper presents a fully automatic pipeline to build a spatio-temporal atlas of ageing bone in the proximal femur. A new technique, termed DXA region free analysis (DXA RFA), is proposed to eliminate morphological variation between DXA scans by warping each image into a reference template. To construct the atlas, we use unprocessed DXA data from Caucasian women aged 20-97 years participating in three cohort studies in Western Europe (n>13,000). A novel calibration procedure, termed quantile matching regression, is proposed to integrate data from different DXA manufacturers. Pixel-wise BMD evolution with ageing was modelled using smooth quantile curves. This technique enables characterisation of spatially-complex BMD change patterns with ageing, visualised using heat-maps. Furthermore, quantile curves plotted at different pixel coordinates showed consistently different rates of bone loss at different regions within the femoral neck. Given the close relationship between spatio-temporal bone loss and osteoporotic fracture, improved understanding of the bone ageing process could lead to enhanced prognostic, preventive and therapeutic strategies for the disease.

$Research paper thumbnail of Local volume fraction distributions of axons, astrocytes, and myelin in deep subcortical white matter$

NeuroImage, Jan 19, 2018

This study aims to statistically describe histologically stained white matter brain sections to s... more This study aims to statistically describe histologically stained white matter brain sections to subsequently inform and validate diffusion MRI techniques. For the first time, we characterise volume fraction distributions of three of the main structures in deep subcortical white matter (axons, astrocytes, and myelinated axons) in a representative cohort of an ageing population for which well-characterized neuropathology data is available. We analysed a set of samples from 90 subjects of the Cognitive Function and Ageing Study (CFAS), stratified into three groups of 30 subjects each, in relation to the presence of age-associated deep subcortical lesions. This provides volume fraction distributions in different scenarios relevant to brain diffusion MRI in dementia. We also assess statistically significant differences found between these groups. In agreement with previous literature, our results indicate that white matter lesions are related with a decrease in the myelinated axons fract...

Journal of Fluid Mechanics, 2017

Flow complexity is related to a number of phenomena in science and engineering and has been appro... more Flow complexity is related to a number of phenomena in science and engineering and has been approached from the perspective of chaotic dynamical systems, ergodic processes or mixing of fluids, just to name a few. To the best of our knowledge, all existing methods to quantify flow complexity are only valid for infinite time evolution, for closed systems or for mixing of two substances. We introduce an index of flow complexity coined interlacing complexity index (ICI), valid for a single-phase flow in an open system with inlet and outlet regions, involving finite times. ICI is based on Shannon’s mutual information (MI), and inspired by an analogy between inlet–outlet open flow systems and communication systems in communication theory. The roles of transmitter, receiver and communication channel are played, respectively, by the inlet, the outlet and the flow transport between them. A perfectly laminar flow in a straight tube can be compared to an ideal communication channel where the t...

PloS one, 2017

Using computational fluid dynamics (CFD) to compute the hemodynamics in cerebral aneurysms has re... more Using computational fluid dynamics (CFD) to compute the hemodynamics in cerebral aneurysms has received much attention in the last decade. The usability of these methods depends on the quality of the computations, highlighted in recent discussions. The purpose of this study is to investigate the convergence of common hemodynamic indicators with respect to numerical resolution. 38 middle cerebral artery bifurcation aneurysms were studied at two different resolutions (one comparable to most studies, and one finer). Relevant hemodynamic indicators were collected from two of the most cited studies, and were compared at the two refinements. In addition, correlation to rupture was investigated. Most of the hemodynamic indicators were very well resolved at the coarser resolutions, correlating with the finest resolution with a correlation coefficient >0.95. The oscillatory shear index (OSI) had the lowest correlation coefficient of 0.83. A logarithmic Bland-Altman plot revealed noticeabl...

Magnetic resonance in medicine, Jan 16, 2017

An emerging topic in diffusion magnetic resonance is imaging blood microcirculation alongside wat... more An emerging topic in diffusion magnetic resonance is imaging blood microcirculation alongside water diffusion using the intravoxel incoherent motion (IVIM) model. Recently, a combined IVIM diffusion tensor imaging (IVIM-DTI) model was proposed, which accounts for both anisotropic pseudo-diffusion due to blood microcirculation and anisotropic diffusion due to tissue microstructures. In this article, we propose a robust IVIM-DTI approach for simultaneous diffusion and pseudo-diffusion tensor imaging. Conventional IVIM estimation methods can be broadly divided into two-step (diffusion and pseudo-diffusion estimated separately) and one-step (diffusion and pseudo-diffusion estimated simultaneously) methods. Here, both methods were applied on the IVIM-DTI model. An improved one-step method based on damped Gauss-Newton algorithm and a Gaussian prior for the model parameters was also introduced. The sensitivities of these methods to different parameter initializations were tested with reali...

Journal of orthopaedic research : official publication of the Orthopaedic Research Society, Oct 7, 2017

Dual energy X-ray absorptiometry (DXA) is the reference standard method used to study bone minera... more Dual energy X-ray absorptiometry (DXA) is the reference standard method used to study bone mineral density (BMD) after total hip arthroplasty (THA). However, the subtle, spatially-complex changes in bone mass due to strain-adaptive bone remodeling relevant to different prosthesis designs are not readily resolved using conventional DXA analysis. DXA region free analysis (DXA RFA) is a novel computational image analysis technique that provides a high-resolution quantitation of periprosthetic BMD. Here we applied the technique to quantitate the magnitude and areal size of periprosthetic BMD changes using scans acquired during two previous randomized clinical trials (2004 to 2009); one comparing three cemented prosthesis design geometries, and the other comparing a hip resurfacing versus a conventional cementless prosthesis. DXA RFA resolved subtle differences in magnitude and area of bone remodeling between prosthesis designs not previously identified in conventional DXA analyses. A me...

Medical image analysis, Jan 9, 2016

Image registration is an essential technique to obtain point correspondences between anatomical s... more Image registration is an essential technique to obtain point correspondences between anatomical structures from different images. Conventional non-rigid registration methods assume a continuous and smooth deformation field throughout the image. However, the deformation field at the interface of different organs is not necessarily continuous, since the organs may slide over or separate from each other. Therefore, imposing continuity and smoothness ubiquitously would lead to artifacts and increased errors near the discontinuity interface. In computational mechanics, the eXtended Finite Element Method (XFEM) was introduced to handle discontinuities without using computational meshes that conform to the discontinuity geometry. Instead, the interpolation bases themselves were enriched with discontinuous functional terms. Borrowing this concept, we propose a multiresolution eXtented Free-Form Deformation (XFFD) framework that seamlessly integrates within and extends the standard Free-Form...

European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society, Sep 1, 2016

The primary goal of this article is to achieve an automatic and objective method to compute the P... more The primary goal of this article is to achieve an automatic and objective method to compute the Pfirrmann's degeneration grade of intervertebral discs (IVD) from MRI. This grading system is used in the diagnosis and management of patients with low back pain (LBP). In addition, biomechanical models, which are employed to assess the treatment on patients with LBP, require this grading value to compute proper material properties. T2-weighted MR images of 48 patients were employed in this work. The 240 lumbar IVDs were divided into a training set (140) and a testing set (100). Three experts manually classified the whole set of IVDs using the Pfirrmann's grading system and the ground truth was selected as the most voted value among them. The developed method employs active contour models to delineate the boundaries of the IVD. Subsequently, the classification is achieved using a trained Neural Network (NN) with eight designed features that contain shape and intensity information ...

AIP Conference Proceedings, 2006

Nature of the problem (science/management/policy) Freshwater ecosystems play a key role in the Eu... more Nature of the problem (science/management/policy) Freshwater ecosystems play a key role in the European nitrogen (N) cycle, both as a reactive agent that transfers, stores and processes • N loadings from the atmosphere and terrestrial ecosystems, and as a natural environment severely impacted by the increase of these loadings. Approaches Th is chapter is a review of major processes and factors controlling N transport and transformations for running waters, standing waters, • groundwaters and riparian wetlands.

Computerized Medical Imaging and Graphics, 2016

A multiple center milestone study of clinical vertebra segmentation is presented in this paper. V... more 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.

Advances in Applied Clifford Algebras, 2001

IEEE transactions on medical imaging, Jan 11, 2015

Statistical shape models (SSM) are used to introduce shape priors in the segmentation of medical ... more Statistical shape models (SSM) are used to introduce shape priors in the segmentation of medical images. However, such models require large training datasets in the case of multiobject structures, since it is required to obtain not only the individual shape variations but also the relative position and orientation among objects. A solution to overcome this limitation is to model each individual shape independently. However, this approach does not take into account the relative position, orientations and shapes among the parts of an articulated object, which may result in unrealistic geometries, such as with object overlaps. In this article, we propose a new Statistical Model, the Statistical Interspace Model (SIM), which provides information about the interaction of all the individual structures by modeling the interspace between them. The SIM is described using relative position vectors between pair of points that belong to different objects that are facing each other. These vector...

Lecture Notes in Computer Science, 2011

Automated anatomical labeling of the arteries forming the Circle of Willis is of great interest a... more Automated anatomical labeling of the arteries forming the Circle of Willis is of great interest as facilitates inter-subject comparison required to discover geometric risk factors for the development of vascular pathologies. In this paper, we present a method for anatomical labeling of vessels forming anterior part of the Circle of Willis by detecting the five main vessel bifurcations. The method is first trained on a set of pre-labeled examples, where it learns local bifurcation features as well as global variation in the anatomy of the extracted vascular trees. Then the labeling of the target vascular tree is formulated as maximum a posteriori solution where the classifications of individual bifurcations are regularized by the prior learned knowledge of the tree they span. The method was evaluated by cross-validation on 30 subjects, which showed the vascular trees were correctly anatomically labeled in 90% of cases. The proposed method can naturally handle anatomical variations and is shown to be suitable for labeling arterial segments of Circle of Willis.

Medical Imaging 2015: Image Processing, 2015

This paper presents a novel method to treat discontinuities in a 3D piece-wise non-rigid registra... more This paper presents a novel method to treat discontinuities in a 3D piece-wise non-rigid registration framework, coined as EXtended Free-Form Deformation (XFFD). Existing discontinuities in the image, such as sliding motion of the lungs or the cardiac boundary adjacent to the blood pool, should be handled to obtain physically plausible deformation fields for motion analysis. However, conventional Free-form deformations (FFDs) impose continuity over the whole image, introducing inaccuracy near discontinuity boundaries. The proposed method incorporates enrichment functions into the FFD formalism, inspired by the linear interpolation method in the EXtended Finite Element Method (XFEM). Enrichment functions enable B-splines to handle discontinuities with minimal increase of computational complexity, while avoiding boundary-matching problem. It retains all properties of the framework of FFDs yet seamlessly handles general discontinuities and can also coexist with other proposed improvements of the FFD formalism. The proposed method showed high performance on synthetic and 3D lung CT images. The target registration error on the CT images is comparable to the previous methods, while being a generic method without assuming any type of motion constraint. Therefore, it does not include any penalty term. However, any of these terms could be included to achieve higher accuracy for specific applications.