Showing papers by "Gemma Piella published in 2016"

Analysis of uncertainty and variability in finite element computational models for biomedical engineering: characterization and propagation

Abstract: Computational modeling has become a powerful tool in biomedical engineering thanks to its potential to simulate coupled systems. However, real parameters are usually not accurately known, and variability is inherent in living organisms. To cope with this, probabilistic tools, statistical analysis and stochastic approaches have been used. This article aims to review the analysis of uncertainty and variability in the context of finite element modeling in biomedical engineering. Characterization techniques and propagation methods are presented, as well as examples of their applications in biomedical finite element simulations. Uncertainty propagation methods, both non-intrusive and intrusive, are described. Finally, pros and cons of the different approaches and their use in the scientific community are presented. This leads us to identify future directions for research and methodological development of uncertainty modeling in biomedical engineering.

Building an Ensemble of Complementary Segmentation Methods by Exploiting Probabilistic Estimates

Abstract: Two common ways of approaching atlas-based segmentation of brain MRI are (1) intensity-based modelling and (2) multi-atlas label fusion. Intensity-based methods are robust to registration errors but need distinctive image appearances. Multi-atlas label fusion can identify anatomical correspondences with faint appearance cues, but needs a reasonable registration. We propose an ensemble segmentation method that combines the complementary features of both types of approaches. Our method uses the probabilistic estimates of the base methods to compute their optimal combination weights in a spatially varying way. We also propose an intensity-based method (to be used as base method) that offers a trade-off between invariance to registration errors and dependence on distinct appearances. Results show that sacrificing invariance to registration errors (up to a certain degree) improves the performance of our intensity-based method. Our proposed ensemble method outperforms the rest of participating methods in most of the structures of the NeoBrainS12 Challenge on neonatal brain segmentation. We achieve up to \(\sim \)10 % of improvement in some structures.

Automatic Model Generation Framework for Computational Simulation of Cochlear Implantation

Abstract: Recent developments in computational modeling of cochlear implantation are promising to study in silico the performance of the implant before surgery. However, creating a complete computational model of the patient’s anatomy while including an external device geometry remains challenging. To address such a challenge, we propose an automatic framework for the generation of patient-specific meshes for finite element modeling of the implanted cochlea. First, a statistical shape model is constructed from high-resolution anatomical μCT images. Then, by fitting the statistical model to a patient’s CT image, an accurate model of the patient-specific cochlea anatomy is obtained. An algorithm based on the parallel transport frame is employed to perform the virtual insertion of the cochlear implant. Our automatic framework also incorporates the surrounding bone and nerve fibers and assigns constitutive parameters to all components of the finite element model. This model can then be used to study in silico the effects of the electrical stimulation of the cochlear implant. Results are shown on a total of 25 models of patients. In all cases, a final mesh suitable for finite element simulations was obtained, in an average time of 94 s. The framework has proven to be fast and robust, and is promising for a detailed prognosis of the cochlear implantation surgery.

Enhanced Probabilistic Label Fusion by Estimating Label Confidences Through Discriminative Learning

Abstract: Multiple-atlas segmentation has recently shown success in automatic segmentation of brain images. It consists in registering the labelmaps from a set of atlases to the anatomy of a target image, and then fusing the multiple labelmaps into a consensus segmentation on the target image. Accurately estimating the confidence of each atlas decision is key for the success of label fusion. Common approaches either rely on local patch similarity, probabilistic statistical frameworks or a combination of both. We present a probabilistic label fusion framework that takes into account label confidence at each point. Maximum likelihood atlas confidences are estimated by explicitly modelling the relationship between image appearance and segmentation errors. We also propose a novel type of label-dependent appearance features based on atlas labelmaps. Our results indicate that the proposed label fusion framework achieves state-of-the-art performance in the segmentation of subcortical structures.

Random walks with shape prior for cochlea segmentation in ex vivo \mu \hbox {CT}

Abstract: Cochlear implantation is a safe and effective surgical procedure to restore hearing in deaf patients. However, the level of restoration achieved may vary due to differences in anatomy, implant type and surgical access. In order to reduce the variability of the surgical outcomes, we previously proposed the use of a high-resolution model built from $$\mu \hbox {CT}$$ images and then adapted to patient-specific clinical CT scans. As the accuracy of the model is dependent on the precision of the original segmentation, it is extremely important to have accurate $$\mu \hbox {CT}$$ segmentation algorithms. We propose a new framework for cochlea segmentation in ex vivo $$\mu \hbox {CT}$$ images using random walks where a distance-based shape prior is combined with a region term estimated by a Gaussian mixture model. The prior is also weighted by a confidence map to adjust its influence according to the strength of the image contour. Random walks is performed iteratively, and the prior mask is aligned in every iteration. We tested the proposed approach in ten $$\mu \hbox {CT}$$ data sets and compared it with other random walks-based segmentation techniques such as guided random walks (Eslami et al. in Med Image Anal 17(2):236–253, 2013) and constrained random walks (Li et al. in Advances in image and video technology. Springer, Berlin, pp 215–226, 2012). Our approach demonstrated higher accuracy results due to the probability density model constituted by the region term and shape prior information weighed by a confidence map. The weighted combination of the distance-based shape prior with a region term into random walks provides accurate segmentations of the cochlea. The experiments suggest that the proposed approach is robust for cochlea segmentation.

Integration of Multi-Plane Tissue Doppler and B-Mode Echocardiographic Images for Left Ventricular Motion Estimation

Abstract: Although modern ultrasound acquisition systems allow recording of 3D echocardiographic images, tracking anatomical structures from them is still challenging. In addition, since these images are typically created from information obtained across several cardiac cycles, it is not yet possible to acquire high-quality 3D images from patients presenting varying heart rhythms. In this paper, we propose a method to estimate the motion field from multi-plane echocardiographic images of the left ventricle, which are acquired simultaneously during a single cardiac cycle. The method integrates tri-plane B-mode and tissue Doppler images acquired at different rotation angles around the long axis of the left ventricle. It uses a diffeomorphic continuous spatio-temporal transformation model with a spherical data representation for a better interpolation in the circumferential direction. This framework allows exploiting the spatial relation among the acquired planes. In addition, higher temporal resolution of the transformation in the beam direction is achieved by uncoupling the estimation of the different components of the velocity field. The method was validated using a realistic synthetic dataset including healthy and ischemic cases, obtaining errors of 0.14 $\pm$ 0.09 mm for displacements, 0.96 $\pm$ 1.03% for longitudinal strain and 3.94 $\pm$ 4.38% for radial strain estimation. In addition, the method was also demonstrated on a healthy volunteer and two patients with ischemia.

Statistical Shape Model with Random Walks for Inner Ear Segmentation

Abstract: Cochlear implants can restore hearing to completely or partially deaf patients. The intervention planning can be aided by providing a patient-specific model of the inner ear. Such a model has to be built from high resolution images with accurate segmentations. Thus, a precise segmentation is required. We propose a new framework for segmentation of micro-CT cochlear images using random walks combined with a statistical shape model (SSM). The SSM allows us to constrain the less contrasted areas and ensures valid inner ear shape outputs. Additionally, a topology preservation method is proposed to avoid the leakage in the regions with no contrast.

Multi-region statistical shape model for cochlear implantation

Abstract: Statistical shape models are commonly used to analyze the variability between similar anatomical structures and their use is established as a tool for analysis and segmentation of medical images. However, using a global model to capture the variability of complex structures is not enough to achieve the best results. The complexity of a proper global model increases even more when the amount of data available is limited to a small number of datasets. Typically, the anatomical variability between structures is associated to the variability of their physiological regions. In this paper, a complete pipeline is proposed for building a multi-region statistical shape model to study the entire variability from locally identified physiological regions of the inner ear. The proposed model, which is based on an extension of the Point Distribution Model (PDM), is built for a training set of 17 high-resolution images (24.5 μm voxels) of the inner ear. The model is evaluated according to its generalization ability and specificity. The results are compared with the ones of a global model built directly using the standard PDM approach. The evaluation results suggest that better accuracy can be achieved using a regional modeling of the inner ear.

Quasi-Conformal Technique for Integrating and Validating Myocardial Tissue Characterization in MRI with Ex-Vivo Human Histological Data

Abstract: Ventricular tachycardia caused by a circuit of re-entry is one of the most critical arrhythmias. It is usually related with heterogeneous scar regions where slow velocity of conduction tissue is mixed with non-conductive tissue, creating pathways (CC) responsible for the tachycardia. Pre-operative DE-MRI can provide information on myocardial tissue viability and then improve therapy planning. However, the current DE-MRI resolution is not sufficient for identifying small CCs and therefore they have to be identified during the intervention, which requires considerable operator experience. In this work, we studied the relationship of histological data (with 10 \(\mu \)m resolution), with in-vivo DE-MRI pixel intensities (PI) of one human heart. Integrating multi-modal data provided by different nature (in- vs. ex-vivo; 3D volume vs. 2D slices) is not straightforward and requires a robust integration pipeline. The main purpose of this work, is to develop a new technique for integrating histological information into the corresponding DE-MRI one. The proposed quasi-conformal mapping technique (QCM) integration were compared with state-of-the-art registration techniques (affine and non-rigid) on a benchmark of 418 synthetically generated datasets showing a more robust results. We used the QCM to quantitatively compare DE-MRI PI with the percentage of fibrosis extracted from histology. We show a positive correlation between the DE-MRI PI and the percentage of fibrosis extracted from histology (r = 0.97; p 60\(\%\) of the maximum intensity value).

Learning pathological deviations from a normal pattern of myocardial motion: Added value for CRT studies?

Abstract: Strong links exist between mechanical dyssynchrony and the response to cardiac resynchronization therapy (CRT). Recent publications recommend identifying correctable dyssynchrony patterns with a specific motion and deformation signature. The learning of these patterns is visual and highly subjective. We take advantage of statistical atlas and dimensionality reduction tools to learn a representation of these patterns. We hypothesize that myocardial motion patterns belong or lie close to a nonlinear manifold, and model them as a pathological deviation from normality. Furthermore, we propose distances to compare new subjects with those patterns and with normality. We evaluate the value of this approach on 2D echocardiographic sequences from CRT candidates at baseline, with pacing on, and at 1-year follow-up. We demonstrate that relating pattern changes with patient response is valuable, and paves the way towards better therapy planning.