Nicholas Ayache

Nicholas Ayache
National Institute for Research in Computer Science and Control | INRIA · Research Field of ICST for Life and Environmental Sciences

PhD

About

943
Publications
80,716
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
43,674
Citations

Publications

Publications (943)
Article
SimulAD is a computational disease progression model (DPM) originally developed on the ADNI database to simulate the evolution of clinical and imaging markers characteristic of AD, and to quantify the disease severity (DS) of a subject. In this work, we assessed the validity of this estimated DS, as well as the generalization of the DPM, by applyin...
Article
Full-text available
In this study we investigate SimulAD, a novel quantitative instrument for the development of intervention strategies for disease modifying drugs in Alzheimer's disease. SimulAD is based on the modeling of the spatio-temporal dynamics governing the joint evolution of imaging and clinical biomarkers along the history of the disease, and allows the si...
Article
Research into artificial intelligence (AI) has made tremendous progress over the past decade. In particular, the AI-powered analysis of images and signals has reached human-level performance in many applications owing to the efficiency of modern machine learning methods, in particular deep learning using convolutional neural networks. Research into...
Article
We propose to learn a probabilistic motion model from a sequence of images for spatio-temporal registration. Our model encodes motion in a low-dimensional probabilistic space – the motion matrix – which enables various motion analysis tasks such as simulation and interpolation of realistic motion patterns allowing for faster data acquisition and da...
Article
Full-text available
We perform unsupervised analysis of image-derived shape and motion features extracted from 3,822 cardiac Magnetic resonance imaging (MRIs) of the UK Biobank. First, with a feature extraction method previously published based on deep learning models, we extract from each case 9 feature values characterizing both the cardiac shape and motion. Second,...
Preprint
Full-text available
Recent failures of clinical trials in Alzheimer’s Disease underline the critical importance of identifying optimal intervention time to maximize cognitive benefit. While several models of disease progression have been proposed, we still lack quantitative approaches simulating the effect of treatment strategies on the clinical evolution. In this wor...
Preprint
We propose to learn a probabilistic motion model from a sequence of images for spatio-temporal registration. Our model encodes motion in a low-dimensional probabilistic space - the motion matrix - which enables various motion analysis tasks such as simulation and interpolation of realistic motion patterns allowing for faster data acquisition and da...
Patent
Systems and methods for performing a medical imaging analysis task using a machine learning based motion model are provided. One or more medical images of an anatomical structure are received. One or more feature vectors are determined. The one or more feature vectors are mapped to one or more motion vectors using the machine learning based motion...
Article
Objective: Test a practical realignment approach to compensate the technical variability of MR radiomic features. Methods: T1 phantom images acquired on 2 scanners, FLAIR and contrast-enhanced T1-weighted (CE-T1w) images of 18 brain tumor patients scanned on both 1.5-T and 3-T scanners, and 36 T2-weighted (T2w) images of prostate cancer patients...
Article
Full-text available
Multiple sclerosis (MS) is a demyelinating and inflammatory disease of the central nervous system (CNS). The demyelination process can be repaired by the generation of a new sheath of myelin around the axon, a process termed remyelination. In MS patients, the demyelination-remyelination cycles are highly dynamic. Over the years, magnetic resonance...
Article
Full-text available
Planning of radiotherapy involves accurate segmentation of a large number of organs at risk (OAR), i.e., organs for which irradiation doses should be minimized to avoid important side effects of the therapy. We propose a deep learning method for segmentation of OAR inside the head, from magnetic resonance images (MRIs). Our system performs segmenta...
Chapter
We propose to learn a probabilistic motion model from a sequence of images. Besides spatio-temporal registration, our method offers to predict motion from a limited number of frames, useful for temporal super-resolution. The model is based on a probabilistic latent space and a novel temporal dropout training scheme. This enables simulation and inte...
Article
Full-text available
We introduce a probabilistic generative model for disentangling spatio-temporal disease trajectories from collections of high-dimensional brain images. The model is based on spatio-temporal matrix factorization, where inference on the sources is constrained by anatomically plausible statistical priors. To model realistic trajectories, the temporal...
Article
Full-text available
Multiple sclerosis (MS) is the most common demyelinating disease. In MS, demyelination occurs in the white matter of the brain and in the spinal cord. It is thus essential to measure the tissue myelin content to understand the physiopathology of MS, track progression and assess treatment efficacy. Positron emission tomography (PET) with [11C]PIB is...
Preprint
We propose to learn a probabilistic motion model from a sequence of images. Besides spatio-temporal registration, our method offers to predict motion from a limited number of frames, useful for temporal super-resolution. The model is based on a probabilistic latent space and a novel temporal dropout training scheme. This enables simulation and inte...
Patent
For registration of medical images with deep learning, a neural network is designed to include a diffeomorphic layer in the architecture. The network may be trained using supervised or unsupervised approaches. By enforcing the diffeomorphic characteristic in the architecture of the network, the training of the network and application of the learned...
Preprint
Planning of radiotherapy involves accurate segmentation of a large number of organs at risk, i.e. organs for which irradiation doses should be minimized to avoid important side effects of the therapy. We propose a deep learning method for segmentation of organs at risk inside the brain region, from Magnetic Resonance (MR) images. Our system perform...
Preprint
In this study we propose a deformation-based framework to jointly model the influence of aging and Alzheimer's disease (AD) on the brain morphological evolution. Our approach combines a spatio-temporal description of both processes into a generative model. A reference morphology is deformed along specific trajectories to match subject specific morp...
Article
In this study we propose a deformation-based framework to jointly model the influence of aging and Alzheimer's disease (AD)on the brain morphological evolution. Our approach combines a spatio-temporal description of both processes into a generative model. A reference morphology is deformed along specific trajectories to match subject specific morph...
Preprint
Full-text available
We introduce a probabilistic generative model for disentangling spatio-temporal disease trajectories from series of high-dimensional brain images. The model is based on spatio-temporal matrix factorization, where inference on the sources is constrained by anatomically plausible statistical priors. To model realistic trajectories, the temporal sourc...
Article
Full-text available
Multiple sclerosis (MS) is a white matter (WM) disease characterized by the formation of WM lesions, which can be visualized by magnetic resonance imaging (MRI). The fluid-attenuated inversion recovery (FLAIR) MRI pulse sequence is used clinically and in research for the detection of WM lesions. However, in clinical settings, some MRI pulse sequenc...
Preprint
We perform unsupervised analysis of image-derived shape and motion features extracted from 3822 cardiac 4D MRIs of the UK Biobank. First, with a feature extraction method previously published based on deep learning models, we extract from each case 9 feature values characterizing both the cardiac shape and motion. Second, a feature selection is per...
Article
We propose to learn a low-dimensional probabilistic deformation model from data which can be used for registration and the analysis of deformations. The latent variable model maps similar deformations close to each other in an encoding space. It enables to compare deformations, generate normal or pathological deformations for any new image or to tr...
Article
We present an efficient deep learning approach for the challenging task of tumor segmentation in multisequence MR images. In recent years, Convolutional Neural Networks (CNN) have achieved state-of-the-art performances in a large variety of recognition tasks in medical imaging. Because of the considerable computational cost of CNNs, large volumes s...
Article
Full-text available
Objective The Multidomain Alzheimer Preventive Trial (MAPT) was designed to assess the effect of omega-3 supplementation and multidomain intervention on cognitive decline of subjects with subjective memory complaint. In term of cognitive testing, no significant effect was found. In this paper, we evaluate the effect of the interventions on the brai...
Preprint
We propose to learn a low-dimensional probabilistic deformation model from data which can be used for registration and the analysis of deformations. The latent variable model maps similar deformations close to each other in an encoding space. It enables to compare deformations, generate normal or pathological deformations for any new image or to tr...
Preprint
Full-text available
Most of the current state-of-the-art methods for tumor segmentation are based on machine learning models trained on manually segmented images. This type of training data is particularly costly, as manual delineation of tumors is not only time-consuming but also requires medical expertise. On the other hand, images with a provided global label (indi...
Article
Full-text available
Personalised cardiac models are a virtual representation of the patient heart, with parameter values for which the simulation fits the available clinical measurements. Models usually have a large number of parameters while the available data for a given patient is typically limited to a small set of measurements, thus the parameters cannot be estim...
Chapter
We propose a deformable registration algorithm based on unsupervised learning of a low-dimensional probabilistic parameterization of deformations. We model registration in a probabilistic and generative fashion, by applying a conditional variational autoencoder (CVAE) network. This model enables to also generate normal or pathological deformations...
Chapter
Alzheimer’s disease (AD) is characterized by complex and largely unknown progression dynamics affecting the brain’s morphology. Although the disease evolution spans decades, to date we cannot rely on long-term data to model the pathological progression, since most of the available measures are on a short-term scale. It is therefore difficult to und...
Chapter
The joint analysis of biomedical data in Alzheimer’s Disease (AD) is important for better clinical diagnosis and to understand the relationship between biomarkers. However, jointly accounting for heterogeneous measures poses important challenges related to the modeling of heterogeneity and to the interpretability of the results. These issues are he...
Chapter
Full-text available
Multiple sclerosis (MS) is a demyelinating disease of the central nervous system (CNS). A reliable measure of the tissue myelin content is therefore essential to understand the physiopathology of MS, track progression and assess treatment efficacy. Positron emission tomography (PET) with \([^{11} \text {C}] \text {PIB}\) has been proposed as a prom...
Preprint
We present an efficient deep learning approach for the challenging task of tumor segmentation in multisequence MR images. In recent years, Convolutional Neural Networks (CNN) have achieved state-of-the-art performances in a large variety of recognition tasks in medical imaging. Because of the considerable computational cost of CNNs, large volumes s...
Conference Paper
Fluid-attenuated inversion recovery (FLAIR) MRI pulse se- quence is used clinically and in research for the detection of WM lesions. However,in a clinical setting, some MRI pulse sequences can be missing because of patient or time constraints. We propose 3D fully convolutional neural networks to predict a FLAIR MRI pulse sequence from other MRI pul...
Article
Objectif En imagerie TEP, les études multicentriques sont limitées car les mesures effectuées sur les images (SUV et autres index radiomiques) sont sensibles aux protocoles d’acquisition et de reconstruction. Notre but est de valider l’utilisation de la méthode d’harmonisation ComBat afin de supprimer l’« effet centre » dans les études multicentriq...
Article
Objectif La caractérisation de l’hétérogénéité tumorale à partir des images TEP connaît un intérêt croissant. Or le lien entre les variables radiomiques (VR) et les caractéristiques biologiques des lésions est encore mal connu. Notre objectif est d’étudier la corrélation entre les VR et les variables métabolomiques (VM) dans le cancer du sein et d’...
Article
Introduction La caractérisation de l’hétérogénéité tumorale à partir des images médicales (appelée aussi radiomique) et de l’extraction de données omiques est un enjeu majeur en cancérologie, notamment dans la mise en place de la médecine de précision. Or actuellement, le lien entre les variables radiomiques (VR) et les caractéristiques biologiques...
Preprint
Full-text available
We propose a method based on deep learning to perform cardiac segmentation on short axis MRI image stacks iteratively from the top slice (around the base) to the bottom slice (around the apex). At each iteration, a novel variant of U-net is applied to propagate the segmentation of a slice to the adjacent slice below it. In other words, the predicti...
Article
Full-text available
Multiple sclerosis (MS) is a demyelinating disease of the central nervous system (CNS). A reliable measure of the tissue myelin content is therefore essential for the understanding of the physiopathology of MS, tracking progression and assessing treatment efficacy. Positron emission tomography (PET) with $[^{11} \mbox{C}] \mbox{PIB}$ has been propo...
Article
Studying organ motion or pathology progression is an important task in diagnosis and therapy of various diseases. Typically, this task is approached by deformable registration of successive images followed by the analysis of the resulting deformation field(s). Most registration methods require prior knowledge in the form of regularization of the im...
Article
Full-text available
We propose a method based on deep learning to perform cardiac segmentation on short axis MRI image stacks iteratively from the top slice (around the base) to the bottom slice (around the apex). At each iteration, a novel variant of U-net is applied to propagate the segmentation of a slice to the adjacent slice below it. In other words, the predicti...
Article
Full-text available
We present a novel automated method to segment the myocardium of both left and right ventricles in MRI volumes. The segmentation is consistent in 3D across the slices such that it can be directly used for mesh generation. Two specific neural networks with multi-scale coarse-to-fine prediction structure are proposed to cope with the small training d...
Article
Full-text available
Goal: We present a model-based feature augmentation scheme to improve the performance of a learning algorithm for the detection of cardiac radio-frequency ablation (RFA) targets with respect to learning from images alone. Methods: Initially, we compute image features from delayed-enhanced MRI (DE-MRI) to describe local tissue heterogeneities and...
Article
Full-text available
The brain is composed of several neural circuits which may be seen as anatomical complexes composed of grey matter structures interconnected by white matter tracts. Grey and white matter components may be modelled as 3D surfaces and curves respectively. Neurodevelopmental disorders involve morphological and organizational alterations which can not...
Article
Full-text available
Personalised computational models of the heart are of increasing interest for clinical applications due to their discriminative and predictive abilities. However, the simulation of a single heartbeat with a 3D cardiac electromechanical model can be long and computationally expensive, which makes some practical applications, such as the estimation o...
Article
Background Radiomics extracts features from medical images more precisely and more accurately than visual assessment. However, radiomics features are affected by CT scanner parameters such as reconstruction kernel or section thickness, thus obscuring underlying biologically important texture features. Purpose To investigate whether a compensation m...
Conference Paper
Robust image registration in medical imaging is essential for comparison or fusion of images, acquired from various perspectives, modalities or at different times. Typically, an objective function needs to be minimized assuming specific a priori deformation models and predefined or learned similarity measures. However, these approaches have difficu...
Conference Paper
Full-text available
Personalised 3D modelling of the heart is of increasing interest in order to better characterise pathologies and predict evolution. The personalisation consists in estimating the parameter values of an electromechanical model in order to reproduce the observed cardiac motion. However, the number of parameters in these models can be high and their e...
Article
Collecting large databases of annotated medical images is crucial for the validation and testing of feature extraction, statistical analysis and machine learning algorithms. Recent advances in cardiac electromechanical modeling and image synthesis provided a framework to generate synthetic images based on realistic mesh simulations. Nonetheless, th...
Conference Paper
In the scope of modelling cardiac electrophysiology (EP) for understanding pathologies and predicting the response to therapies, patient-specific model parameters need to be estimated. Although personalisation from non-invasive data (body surface potential mapping, BSPM) has been investigated on simple cases mostly with a single pacing site, there...
Conference Paper
Computer models of the heart are of increasing interest for clinical applications due to their discriminative and predictive abilities. However the number of simulation parameters in these models can be high and expert knowledge is required to properly design studies involving these models, and analyse the results. In particular it is important to...
Article
The aim of this study is to define an automated and reproducible framework for cochlear anatomical analysis from high-resolution segmented images and to provide a comprehensive and objective shape variability study suitable for cochlear implant design and surgery planning. For the scala tympani (ST), the scala vestibuli (SV) and the whole cochlea,...
Article
Full-text available
This paper presents a simulator tool that can simulate large databases of visually realistic longitudinal MRIs with known volume changes. The simulator is based on a previously proposed biophysical model of brain deformation due to atrophy in AD. In this work, we propose a novel way of reproducing realistic intensity variation in longitudinal brain...
Conference Paper
Modelling the cardiac electrophysiology (EP) can help understand pathologies and predict the response to therapies such as cardiac resynchronization. To this end, estimating patient-specific model parameters is crucial. In the case of patients with bundle branch blocks (BBB), part of the Purkinje system is often affected. The aim of this work is to...
Conference Paper
Real-time MRI-guided electrophysiology (EP) interventions hold the potential to replace conventional X-ray guided procedures aimed to eliminate potentially lethal scar-related arrhythmia. Furthermore, although cardiac MR can provide excellent structural information (i.e., anatomy and scar), these catheter-based procedures have limited electrical in...
Article
Purpose: We aim at developing a framework for the validation of a subject-specific multi-physics model of liver tumor radiofrequency ablation (RFA). Methods: The RFA computation becomes subject specific after several levels of personalization: geometrical and biophysical (hemodynamics, heat transfer and an extended cellular necrosis model). We p...
Article
Modelling cardiac electrophysiology (EP) can help understand pathologies and predict the response to therapies. Moreover, estimating patient-specific parameters of the EP model is crucial to obtain personalised information. The novelty of this paper is to use non-invasive data (body surface potential mapping, BSPM) in order to personalise the main...
Article
In this article, we propose a proof of concept for the automatic planning of personalized radiotherapy for brain tumors. A computational model of glioblastoma growth is combined with an exponential cell survival model to describe the effect of radiotherapy. The model is personalized to the magnetic resonance images (MRIs) of a given patient. It tak...
Article
We investigate uncertainty quantification under a sparse Bayesian model of medical image registration. Bayesian modelling has proven powerful to automate the tuning of registration hyperparameters, such as the trade-off between the data and regularization functionals. Sparsity-inducing priors have recently been used to render the parametrization it...
Conference Paper
Cochlear implants (CI) are used to treat severe hearing loss by surgically inserting an electrode array into the cochlea. Since current electrodes are designed with various insertion depth, ENT surgeons must choose the implant that will maximise the insertion depth without causing any trauma based on preoperative CT images. In this paper, we propos...
Conference Paper
Computer models of the heart are of increasing interest for clinical applications due to their discriminative and predictive abilities. However a single 3D simulation can be computationally expensive and long, which can make some practical applications such as the personalisation phase, or a sensitivity analysis of mechanical parameters over the si...
Article
Full-text available
Esophageal adenocarcinoma arises from Barrett's esophagus, which is the most serious complication of gastroesophageal reflux disease. Strategies for screening involve periodic surveillance and tissue biopsies. A major challenge in such regular examinations is to record and track the disease evolution and re-localization of biopsied sites to provide...
Article
Full-text available
The goal of this study was to evaluate, in the hands of an inexperienced surgeon, the cochleostomy location of an endaural approach (MINV) compared to the conventional posterior tympanotomy (MPT) approach. Since 2010, we use in the ENT department of Nice a new surgical endaural approach to perform cochlear implantation. In the hands of an inexperie...