Quantitative magnetic resonance image analysis via the EM algorithm with stochastic variation

Quantitative Magnetic Resonance Imaging (qMRI) provides researchers insight into pathological and physiological alterations of living tissue, with the help of which researchers hope to predict (local) therapeutic efficacy early and determine optimal treatment schedule. However, the analysis of qMRI has been limited to ad-hoc heuristic methods. Our research provides a powerful statistical framework for image analysis and sheds light on future localized adaptive treatment regimes tailored to the individual's response. We assume in an imperfect world we only observe a blurred and noisy version of the underlying pathological/physiological changes via qMRI, due to measurement errors or unpredictable influences. We use a hidden Markov random field to model the spatial dependence in the data and develop a maximum likelihood approach via the Expectation--Maximization algorithm with stochastic variation. An important improvement over previous work is the assessment of variability in parameter estimation, which is the valid basis for statistical inference. More importantly, we focus on the expected changes rather than image segmentation. Our research has shown that the approach is powerful in both simulation studies and on a real dataset, while quite robust in the presence of some model assumption violations.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS157 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Estimating the granularity coefficient of a Potts-Markov random field within an MCMC algorithm

This paper addresses the problem of estimating the Potts parameter B jointly with the unknown parameters of a Bayesian model within a Markov chain Monte Carlo (MCMC) algorithm. Standard MCMC methods cannot be applied to this problem because performing inference on B requires computing the intractable normalizing constant of the Potts model. In the proposed MCMC method the estimation of B is conducted using a likelihood-free Metropolis-Hastings algorithm. Experimental results obtained for synthetic data show that estimating B jointly with the other unknown parameters leads to estimation results that are as good as those obtained with the actual value of B. On the other hand, assuming that the value of B is known can degrade estimation performance significantly if this value is incorrect. To illustrate the interest of this method, the proposed algorithm is successfully applied to real bidimensional SAR and tridimensional ultrasound images

Accuracy of MAP segmentation with hidden Potts and Markov mesh prior models via Path Constrained Viterbi Training, Iterated Conditional Modes and Graph Cut based algorithms

In this paper, we study statistical classification accuracy of two different Markov field environments for pixelwise image segmentation, considering the labels of the image as hidden states and solving the estimation of such labels as a solution of the MAP equation. The emission distribution is assumed the same in all models, and the difference lays in the Markovian prior hypothesis made over the labeling random field. The a priori labeling knowledge will be modeled with a) a second order anisotropic Markov Mesh and b) a classical isotropic Potts model. Under such models, we will consider three different segmentation procedures, 2D Path Constrained Viterbi training for the Hidden Markov Mesh, a Graph Cut based segmentation for the first order isotropic Potts model, and ICM (Iterated Conditional Modes) for the second order isotropic Potts model. We provide a unified view of all three methods, and investigate goodness of fit for classification, studying the influence of parameter estimation, computational gain, and extent of automation in the statistical measures Overall Accuracy, Relative Improvement and Kappa coefficient, allowing robust and accurate statistical analysis on synthetic and real-life experimental data coming from the field of Dental Diagnostic Radiography. All algorithms, using the learned parameters, generate good segmentations with little interaction when the images have a clear multimodal histogram. Suboptimal learning proves to be frail in the case of non-distinctive modes, which limits the complexity of usable models, and hence the achievable error rate as well. All Matlab code written is provided in a toolbox available for download from our website, following the Reproducible Research Paradigm

Temporal and Spatial Data Mining with Second-Order Hidden Models

In the frame of designing a knowledge discovery system, we have developed stochastic models based on high-order hidden Markov models. These models are capable to map sequences of data into a Markov chain in which the transitions between the states depend on the \texttt{n} previous states according to the order of the model. We study the process of achieving information extraction fromspatial and temporal data by means of an unsupervised classification. We use therefore a French national database related to the land use of a region, named Teruti, which describes the land use both in the spatial and temporal domain. Land-use categories (wheat, corn, forest, ...) are logged every year on each site regularly spaced in the region. They constitute a temporal sequence of images in which we look for spatial and temporal dependencies. The temporal segmentation of the data is done by means of a second-order Hidden Markov Model (\hmmd) that appears to have very good capabilities to locate stationary segments, as shown in our previous work in speech recognition. Thespatial classification is performed by defining a fractal scanning ofthe images with the help of a Hilbert-Peano curve that introduces atotal order on the sites, preserving the relation ofneighborhood between the sites. We show that the \hmmd performs aclassification that is meaningful for the agronomists.Spatial and temporal classification may be achieved simultaneously by means of a 2 levels \hmmd that measures the \aposteriori probability to map a temporal sequence of images onto a set of hidden classes

Recursive image sequence segmentation by hierarchical models

This paper addresses the problem of image sequence segmentation. A technique using a sequence model based on compound random fields is presented. This technique is recursive in the sense that frames are processed in the same cadency as they are produced. New regions appearing in the sequence are detected by a morphological procedure.Peer ReviewedPostprint (published version