Heterogeneous Porous Media Simulation

Intracranial aneurysms are vascular disorders in which weakness in the wall of a cerebral artery or vein causes a localized dilation of the blood vessel. Flow diversion is an endovascular technique where a flow diverter stent is placed in the parent blood vessel to divert blood flow away from the aneurysm itself. Simulation by computational fluid dynamics is an attractive method to study flow diverters, particularly to model the small gaps between stent struts as a porous media. In many cases obstructions are not equal across the free medium and the porous one must be heterogeneous. Finite Volume Method solves numerical problems of computational fluid dynamics, splitting the region of interest in cells of small volumes. Porous media are usually modeled as a set of simulation cells described in a dictionary with constant porosity parameters (Homogeneous medium). An heterogeneous medium can be described as multiple homogeneous media, one by one. However, creating multiple homogeneous porous media is a tedious job if each simulation cell requires different parameters. Also, porous medium sets creates overheads on memory and processor load. The open source tool OpenFOAM is a open source C++ toolbox for field operations and partial differential equations solving using Finite Volume Method, including computational fluid dynamics. The tool is well prepared to describe heterogeneous fields. In this work, porous media coefficients are described as tensor fields. A steady state flow solver considering this fields is developed. The fidelity of the solver is then studied qualitatively and quantitatively.Fil: Dazeo, Nicolás Ignacio. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; ArgentinaFil: Dottori, Javier Alejandro. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; ArgentinaFil: Boroni, Gustavo Adolfo. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; ArgentinaFil: Larrabide, Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; Argentin

Evaluating sleep-stage classification: how age and early-late sleep affects classification performance

Sleep stage classification is a common method used by experts to monitor the quantity and quality of sleep in humans, but it is a time-consuming and labour-intensive task with high inter- and intra-observer variability. Using Wavelets for feature extraction and Random Forest for classification, an automatic sleep-stage classification method was sought and assessed. The age of the subjects, as well as the moment of sleep (early-night and late-night), were confronted to the performance of the classifier. From this study, we observed that these variables do affect the automatic model performance, improving the classification of some sleep stages and worsening others

A ResNet is All You Need? Modeling A Strong Baseline for Detecting Referable Diabetic Retinopathy in Fundus Images

Deep learning is currently the state-of-the-art for automated detection of referable diabetic retinopathy (DR) from color fundus photographs (CFP). While the general interest is put on improving results through methodological innovations, it is not clear how good these approaches perform compared to standard deep classification models trained with the appropriate settings. In this paper we propose to model a strong baseline for this task based on a simple and standard ResNet-18 architecture. To this end, we built on top of prior art by training the model with a standard preprocessing strategy but using images from several public sources and an empirically calibrated data augmentation setting. To evaluate its performance, we covered multiple clinically relevant perspectives, including image and patient level DR screening, discriminating responses by input quality and DR grade, assessing model uncertainties and analyzing its results in a qualitative manner. With no other methodological innovation than a carefully designed training, our ResNet model achieved an AUC = 0.955 (0.953 - 0.956) on a combined test set of 61007 test images from different public datasets, which is in line or even better than what other more complex deep learning models reported in the literature. Similar AUC values were obtained in 480 images from two separate in-house databases specially prepared for this study, which emphasize its generalization ability. This confirms that standard networks can still be strong baselines for this task if properly trained.Comment: Accepted for publication at the 18th International Symposium on Medical Information Processing and Analysis (SIPAIM 2022

Lumen-intima and media-adventitia segmentation in IVUS images using supervised classifications of arterial layers and morphological structures

Background: Intravascular ultrasound (IVUS) provides axial grey-scale images of blood vessels. The large number of images require automatic analysis, specifically to identify the lumen and outer vessel wall. However, the high amount of noise, the presence of artifacts and anatomical structures, such as bifurcations, calcifications and fibrotic plaques, usually hinder the proper automatic segmentation of the vessel wall. Methods: Lumen, media, adventitia and surrounding tissues are automatically detected using Support Vector Machines (SVMs). The classification performance of the SVMs vary according to the kind of structure present within each region of the image. Random Forest (RF) is used to detect different morphological structures and to modify the initial layer classification depending on the detected structure. The resulting classification maps are fed into a segmentation method based on deformable contours to detect lumen-intima (LI) and media-adventitia (MA) interfaces. Results: The modifications in the layer classifications according to the presence of structures proved to be effective improving LI and MA segmentations. The proposed method reaches a Jaccard Measure (JM) of 0.88 ± 0.08 for LI segmentation, compared with 0.88 ± 0.05 of a semiautomatic method. When looking at MA, our method reaches a JM of 0.84 ± 0.09, and outperforms previous automatic methods in terms of HD, with 0.51mm ± 0.30. Conclusions: A simple modification to the arterial layer classification produces results that match and improve state-of-the-art fully-automatic segmentation methods for LI and MA in 20MHz IVUS images. For LI segmentation, the proposed automatic method performs accurately as semi-automatic methods. For MA segmentation, our method matched the quality of state-of-the-art automatic methods described in the literature. Furthermore, our implementation is modular and open-source, allowing for future extensions and improvements.Fil: Lo Vercio, Lucas. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; ArgentinaFil: del Fresno, Mirta Mariana. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; ArgentinaFil: Larrabide, Ignacio. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentin

Stenting as porous media in anatomically accurate geometries: A comparison of models and spatial heterogeneity

Modelling intracranial aneurysm blood flow after flow diverter treatment has proven to be of great scientific and clinical interest. One of the reasons for not having CFD as an everyday clinical tool yet is the time required to set-up such simulations plus the required computational time. The speed-up of these simulations can have a considerable impact during treatment planning and device selection. Modelling flow diverters as a porous medium (PM) can considerably improve the computational time. Many models have been presented in literature, but quantitative comparisons between models are scarce.In this study, the untreated case, the explicit definition of the flow diverter wires as no-slip boundary condition and five different porous medium models were chosen for comparison, and evaluated on intracranial aneurysm of 14 patients with different shapes, sizes, and locations. CFD simulations were made using finite volume method on steady flow conditions. Velocities, kinetic energy, wall shear stress, and computational time were assessed for each model. Then, all models are compared against the no-slip boundary condition using non parametric Kolmogorov–Smirnov test.The model with least performance showed a mean K-S statistic of 0.31 and deviance of 0.2, while the model with best values always gave K-S statistics below 0.2. Kinetic energy between PM models varied between an over estimation of 218.3% and an under estimation of 73.06%. Also, speedups were between 4.75x and 5.3x (stdev: 0.38x and 0.15x) when using PM models.Flow diverters can be simulated with PM with a good agreement to standard CFD simulations were FD wires are represented with no-slip boundary condition in less than a quarter of the time. Best results were obtained on PM models based on geometrical properties, in particular, when using a heterogeneous medium based on equations for flat rhomboidal wire frames.Fil: Dazeo, Nicolás Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; ArgentinaFil: Dottori, Javier Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; ArgentinaFil: Boroni, Gustavo Adolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; ArgentinaFil: Narata, Ana Paula. Universite de Tours; FranciaFil: Larrabide, Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; Argentin

Learning normal asymmetry representations for homologous brain structures

Although normal homologous brain structures are approximately symmetrical by definition, they also have shape differences due to e.g. natural ageing. On the other hand, neurodegenerative conditions induce their own changes in this asymmetry, making them more pronounced or altering their location. Identifying when these alterations are due to a pathological deterioration is still challenging. Current clinical tools rely either on subjective evaluations, basic volume measurements or disease-specific deep learning models. This paper introduces a novel method to learn normal asymmetry patterns in homologous brain structures based on anomaly detection and representation learning. Our framework uses a Siamese architecture to map 3D segmentations of left and right hemispherical sides of a brain structure to a normal asymmetry embedding space, learned using a support vector data description objective. Being trained using healthy samples only, it can quantify deviations-from-normal-asymmetry patterns in unseen samples by measuring the distance of their embeddings to the center of the learned normal space. We demonstrate in public and in-house sets that our method can accurately characterize normal asymmetries and detect pathological alterations due to Alzheimer’s disease and hippocampal sclerosis, even though no diseased cases were accessed for training. Our source code is available at https://github.com/duiliod/DeepNORH

Learning normal asymmetry representations for homologous brain structures

Although normal homologous brain structures are approximately symmetrical by definition, they also have shape differences due to e.g. natural ageing. On the other hand, neurodegenerative conditions induce their own changes in this asymmetry, making them more pronounced or altering their location. Identifying when these alterations are due to a pathological deterioration is still challenging. Current clinical tools rely either on subjective evaluations, basic volume measurements or disease-specific deep learning models. This paper introduces a novel method to learn normal asymmetry patterns in homologous brain structures based on anomaly detection and representation learning. Our framework uses a Siamese architecture to map 3D segmentations of left and right hemispherical sides of a brain structure to a normal asymmetry embedding space, learned using a support vector data description objective. Being trained using healthy samples only, it can quantify deviations-from-normal-asymmetry patterns in unseen samples by measuring the distance of their embeddings to the center of the learned normal space. We demonstrate in public and in-house sets that our method can accurately characterize normal asymmetries and detect pathological alterations due to Alzheimer's disease and hippocampal sclerosis, even though no diseased cases were accessed for training. Our source code is available at https://github.com/duiliod/DeepNORHA

NORHA: A NORmal Hippocampal Asymmetry Deviation Index Based on One-Class Novelty Detection and 3D Shape Features

Radiologists routinely analyze hippocampal asymmetries in magnetic resonance (MR) images as a biomarker for neurodegenerative conditions like epilepsy and Alzheimer’s Disease. However, current clinical tools rely on either subjective evaluations, basic volume measurements, or disease-specific models that fail to capture more complex differences in normal shape. In this paper, we overcome these limitations by introducing NORHA, a novel NORmal Hippocampal Asymmetry deviation index that uses machine learning novelty detection to objectively quantify it from MR scans. NORHA is based on a One-Class Support Vector Machine model learned from a set of morphological features extracted from automatically segmented hippocampi of healthy subjects. Hence, in test time, the model automatically measures how far a new unseen sample falls with respect to the feature space of normal individuals. This avoids biases produced by standard classification models, which require being trained using diseased cases and therefore learning to characterize changes produced only by the ones. We evaluated our new index in multiple clinical use cases using public and private MRI datasets comprising control individuals and subjects with different levels of dementia or epilepsy. The index reported high values for subjects with unilateral atrophies and remained low for controls or individuals with mild or severe symmetric bilateral changes. It also showed high AUC values for discriminating individuals with hippocampal sclerosis, further emphasizing its ability to characterize unilateral abnormalities. Finally, a positive correlation between NORHA and the functional cognitive test CDR-SB was observed, highlighting its promising application as a biomarker for dementia.La versión final de este artículo fue publicada el 29 de junio de 2023 en Brain Topography (Springer). Se encuentra accesible desde Biblioteca Di Tella a través de Prim

Carotid Intima Media Thickness Reference Intervals for a Healthy Argentinean Population Aged 11-81 Years

Reference intervals (RIs) of carotid intima media thickness (CIMT) from large healthy population are still lacking in Latin America. The aim of this study was to determine CIMT RIs in a cohort of 1012 healthy subjects from Argentina. We evaluated if RIs for males and females and for left and right carotids were necessary. Second, mean and standard deviation (SD) age-related equations were obtained for left, right, and average (left + right)/2) CIMT using parametric regression methods based on fractional polynomials, in order to obtain age-specific percentiles curves. Age-specific percentile curves were obtained. Males showed higher A-CIMT ( mm versus  mm, ) in comparison with females. For males, the equations were as follows: A-CIMT mean = 0.42 + ; A-CIMT SD = 5.9 × 10−2 + . For females, they were as follows: A-CIMT mean = 0.40 + ; A-CIMT SD = 4.67 × 10−2 + . Our study provides the largest database concerning RIs of CIMT in healthy people in Argentina. Specific RIs and percentiles of CIMT for children, adolescents, and adults are now available according to age and gender, for right and left common carotid arteries.Fil: Diaz, Alberto Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires; ArgentinaFil: Bia, Daniel. Universidad de la República; UruguayFil: Zócalo, Yanina. Universidad de la República; UruguayFil: Manterola, Hugo Luis. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Larrabide, Ignacio. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lo Vercio, Lucas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas; ArgentinaFil: del Fresno, Mirta Mariana. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cabrera Fischer, Edmundo Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Medicina Traslacional, Trasplante y Bioingeniería. Fundación Favaloro. Instituto de Medicina Traslacional, Trasplante y Bioingeniería; Argentin