Medical imaging studies often rely on a single sample per subject, assuming it is representative of their physiological traits. However, variations in how input descriptors are defined or computed (e.g. due to a lack of consensus in the scientific field) may have a crucial impact on the analysis, and are hardly considered in practice. In this paper, we propose an original strategy based on representation learning to estimate a parametric map reflecting the impact of such definitional differences on a given physiological descriptor, previously extracted from medical images. We consider the different definitions or computations of such physiological descriptors as different high-dimensional data, potentially of heterogeneous types. We specifically focus on myocardial deformation (strain), for which there is limited agreement on its definition. We first use manifold alignment to match the latent representations associated with the different definitions of this descriptor. Then, we formulate plausible distributions in the latent space to represent definitional divergence across descriptors, from which we reconstruct a high-dimensional parametric map to visualize such definitional divergence. Due to the lack of proper ground truth for this specific clinical application, we first demonstrate this methodology on toy experiments and then expand the evaluation on right ventricular strain data from subjects obtained from 3D echocardiographic image sequences, for which different types of strain are available at each point of the right ventricle endocardial surface mesh. Beyond this illustrative application, our methodology has the potential to be generalised to many other population analyses considering heterogeneous high-dimensional descriptors.

Cardiac imaging protocols usually result in several types of acquisitions and descriptors extracted from the images. The statistical analysis of such data across a population may be challenging, and can be addressed by fusion techniques within a dimensionality reduction framework. However, directly combining different data types may lead to unfair comparisons (for heterogeneous descriptors) or over-exploitation of information (for strongly correlated modalities). In contrast, physicians progressively consider each type of data based on hierarchies derived from their experience or evidence-based recommendations, an inspiring approach for data fusion strategies. In this paper, we propose a novel methodology for hierarchical data fusion and unsupervised representation learning. It mimics the physicians' approach by progressively integrating different high-dimensional data descriptors according to a known hierarchy. We model this hierarchy with a Hierarchical Gaussian Process Latent Variable Model (GP-LVM), which links the estimated low-dimensional latent representation and high-dimensional observations at each level in the hierarchy, with additional links between consecutive levels of the hierarchy. We demonstrate the relevance of this approach on a dataset of 1726 magnetic resonance image slices from 123 patients revascularized after acute myocardial infarction (MI) (first level in the hierarchy), some of them undergoing reperfusion injury (microvascular obstruction (MVO), second level in the hierarchy). Our experiments demonstrate that our hierarchical model provides consistent data organization across levels of the hierarchy and according to physiological characteristics of the lesions. This allows more relevant statistical analysis of myocardial lesion patterns, and in particular subtle lesions such as MVO.

Cardiac myofibre deformation is an important determinant of the mechanical function of the heart. Quantification of myofibre strain relies on 3D measurements of ventricular wall motion interpreted with respect to the tissue microstructure. In this study, we estimated in vivo myofibre strain using 3D structural and functional atlases of the human heart. A finite element modelling framework was developed to incorporate myofibre orientations of the left ventricle (LV) extracted from 7 explanted normal human hearts imaged ex vivo with diffusion tensor magnetic resonance imaging (DTMRI) and kinematic measurements from 7 normal volunteers imaged in vivo with tagged MRI. Myofibre strain was extracted from the DTMRI and 3D strain from the tagged MRI. We investigated: i) the spatio-temporal variation of myofibre strain throughout the cardiac cycle; ii) the sensitivity of myofibre strain estimates to the variation in myofibre angle between individuals; and iii) the sensitivity of myofibre strain estimates to variations in wall motion between individuals. Our analysis results indicate that end systolic (ES) myofibre strain is approximately homogeneous throughout the entire LV, irrespective of the inter-individual variation in myofibre orientation. Additionally, inter-subject variability in myofibre orientations has greater effect on the variabilities in myofibre strain estimates than the ventricular wall motions. This study provided the first quantitative evidence of homogeneity of ES myofibre strain using minimally-invasive medical images of the human heart and demonstrated that image-based modelling framework can provide detailed insight to the mechanical behaviour of the myofibres, which may be used as a biomarker for cardiac diseases that affect cardiac mechanics.

We present an optical flow technique in a differential projected framework adapted to local myocardial motion estimation from MR Tagged images. The algorithm is based on the Dual Tree design of Hilbert transform pairs of wavelet bases. Such a design allows one to construct several orientation-sensitive wavelet filters for better analysis of the complex motion of the heart. The complex wavelet transform (CWT) integrates both energy and phase information in the wavelets coefficients for an effective motion estimation. The CWT also provides a high frequency analysis and enjoys a multiresolution aspect that allows multiscale flow estimate. Performances of the algorithm are evaluated on synthetic tagged MRI sequences for both displacement and strain estimation.

In this paper, we consider the estimation of a reference shape from a set of different segmentation results using both active contours and information theory. The reference shape is defined as the minimum of a criterion that benefits from both the mutual information and the joint entropy of the input segmentations and is then called a mutual shape. This energy criterion is here justified using similarities between information theory quantities and area measures, and presented in a continuous variational framework. This framework brings out some interesting evaluation measures such as the specificity and sensitivity. In order to solve this shape optimization problem, shape derivatives are computed for each term of the criterion and interpreted as an evolution equation of an active contour. Some synthetical examples allow us to cast the light on the difference between our mutual shape and an average shape. Our framework has been considered for the estimation of a mutual shape for the evaluation of cardiac segmentation methods in MRI.

This paper presents the Virtual Imaging Platform (VIP), a platform accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011.

A statistical methodology is proposed to rank several estimation methods of a relevant clinical parameter when no gold standard is available. Based on a regression without truth method, the proposed approach was applied to rank eight methods without using any a priori information regarding the reliability of each method and its degree of automation. It was only based on a prior concerning the statistical distribution of the parameter of interest in the database. The ranking of the methods relies on figures of merit derived from the regression and computed using a bootstrap process. The methodology was applied to the estimation of the left ventricular ejection fraction derived from cardiac magnetic resonance images segmented using eight approaches with different degrees of automation: three segmentations were entirely manually performed and the others were variously automated. The ranking of methods was consistent with the expected performance of the estimation methods: the most accurate estimates of the ejection fraction were obtained using manual segmentations. The robustness of the ranking was demonstrated when at least three methods were compared. These results suggest that the proposed statistical approach might be helpful to assess the performance of estimation methods on clinical data for which no gold standard is available.

Cardiac fibers, as well as their local arrangement in laminar sheets, have a complex spatial variation of their orientation that has an important role in mechanical and electrical cardiac functions. In this paper, a statistical atlas of this cardiac fiber architecture is built for the first time using human datasets. This atlas provides an average description of the human cardiac fiber architecture along with its variability within the population. In this study, the population is composed of ten healthy human hearts whose cardiac fiber architecture is imaged ex vivo with DT-MRI acquisitions. The atlas construction is based on a computational framework that minimizes user interactions and combines most recent advances in image analysis: graph cuts for segmentation, symmetric log-domain diffeomorphic demons for registration, and log-Euclidean metric for diffusion tensor processing and statistical analysis. Results show that the helix angle of the average fiber orientation is highly correlated to the transmural depth and ranges from -41° on the epicardium to +66° on the endocardium. Moreover, we find that the fiber orientation dispersion across the population (±13°) is lower than for the laminar sheets (±31°) . This study, based on human hearts, extends previous studies on other mammals with concurring conclusions and provides a description of the cardiac fiber architecture more specific to human and better suited for clinical applications. Indeed, this statistical atlas can help to improve the computational models used for radio-frequency ablation, cardiac resynchronization therapy, surgical ventricular restoration, or diagnosis and followups of heart diseases due to fiber architecture anomalies.

Medical image simulation produces virtual images from software representations of imaging devices and virtual object models representing the human body. Object models consist of the geometry of the objects (e.g. organs, tissues, pathological structures, etc.) and of their physical parameters used for the simulation. The diversity of this information makes it difficult to share and reuse across simulation modalities and users. We address this issue by explicitly describing object models using a semantic approach. In particular, we developed an ontology that contains the relevant concepts and relations of the domain of object models for image simulation. This ontology is used to annotate object models and to describe their content and structure. In this paper, we present the construction steps of this ontology, the representation choices and we illustrate how it is used to annotate object models.

This paper describes a framework for the integration of medical image simulators in the Virtual Imaging Platform (VIP). Simulation is widely involved in medical imaging but its availability is hampered by the heterogeneity of software interfaces and the required amount of computing power. To address this, VIP defines a simulation workflow template which transforms object models from the IntermediAte Model Format (IAMF) into native simulator formats and parallelizes the simulation computation. Format conversions, geometrical scene definition and physical parameter generation are covered. The core simulator executables are directly embedded in the simulation workflow, enabling data parallelism exploitation without modifying the simulator. The template is instantiated on simulators of the four main medical imaging modalities, namely Positron Emission Tomography, Ultrasound imaging, Magnetic Resonance Imaging and Computed Tomography. Simulation examples and performance results on the European Grid Infrastructure are shown.

Segmenting 3D images is critical in medical imaging but the parameterization of segmentation algorithms is difficult due to their computation heaviness and complex interactions between the parameters. This paper targets the exploration of deformable-model-based segmentation parameter spaces to search for salient ranges. We propose a framework exploring the parameter space with a genetic algorithm and interactively clustering the segmentation results. The framework only requires a limited number of parameters, it does not make any assumption on the segmentation algorithm and it does not require any ground truth or gold standard. Results obtained on a 3D image of the heart show that the proposed method has good robustness capabilities and that it is able to efficiently exhibit interesting parameter ranges.

The new SinMod method extracts motion from magnetic resonance imaging (MRI)-tagged (MRIT) image sequences. Image intensity in the environment of each pixel is modeled as a moving sine wavefront. Displacement is estimated at subpixel accuracy. Performance is compared with the harmonic-phase analysis (HARP) method, which is currently the most common method used to detect motion in MRIT images. SinMod can handle line tags, as well as speckle patterns. In artificial images (tag distance six pixels), SinMod detects displacements accurately (error < 0.02 pixels). Effects of noise are suppressed effectively. Sharp transitions in motion at the boundary of an object are smeared out over a width of 0.6 tag distance. For MRIT images of the heart, SinMod appears less sensitive to artifacts, especially later in the cardiac cycle when image quality deteriorates. For each pixel, the quality of the sine-wave model in describing local image intensity is quantified objectively. If local quality is low, artifacts are avoided by averaging motion over a larger environment. Summarizing, SinMod is just as fast as HARP, but it performs better with respect to accuracy of displacement detection, noise reduction, and avoidance of artifacts.

A new neural network-based approach is proposed to estimate motion hierarchy in image sequences taking into consideration motion discontinuities. The network consists in an input layer, an intermediate layer and an output layer. In order to estimate the most likely displacement at each pixel, we have transposed the block matching approach into the neural network approach and add mechanisms to detect motion discontinuities. Information redundancy allows for parallel processing in view of real-time complex motion estimation tasks. Preliminary tests on synthetic and real images are very promising.

We consider a recent parametric level-set segmentation approach where the implicit interface is the zero level of a continuous function expanded onto compactly supported radial basis functions, defined by their centers, coefficients and supports. We propose to introduce prior knowledge of the shape to be recovered by placing the centers quasi-uniformly over an uncertainty area.

Motion estimation is an important issue in radiation therapy of moving organs. In particular, motion estimates from 4-D imaging can be used to compute the distribution of an absorbed dose during the therapeutic irradiation. We propose a strategy and criteria incorporating spatiotemporal information to evaluate the accuracy of model-based methods capturing breathing motion from 4-D CT images. This evaluation relies on the identification and tracking of landmarks on the 4-D CT images by medical experts. Three different experts selected more than 500 landmarks within 4-D CT images of lungs for three patients. Landmark tracking was performed at four instants of the expiration phase. Two metrics are proposed to evaluate the tracking performance of motion-estimation models. The first metric cumulates over the four instants the errors on landmark location. The second metric integrates the error over a time interval according to an a priori breathing model for the landmark spatiotemporal trajectory. This latter metric better takes into account the dynamics of the motion. A second aim of this paper is to estimate the impact of considering several phases of the respiratory cycle as compared to using only the extreme phases (end-inspiration and end-expiration). The accuracy of three motion estimation models (two image registration-based methods and a biomechanical method) is compared through the proposed metrics and statistical tools. This paper points out the interest of taking into account more frames for reliably tracking the respiratory motion.

Digital medical image processing is a promising application area for grids. Given the volume of data, the sensitivity of medical information, and the joint complexity of medical datasets and computations expected in clinical practice, the challenge is to fill the gap between the grid middleware and the requirements of clinical applications. The research project AGIR (Grid Analysis of Radiological Data) presented in this paper addresses this challenge through a combined approach: on one hand, leveraging the grid middleware through core grid medical services which target the requirements of medical data processing applications; on the other hand, grid-enabling a panel of applications ranging from algorithmic research to clinical applications.

A new approach for correcting bias field in magnetic resonance (MR) images is proposed using the mathematical model of singularity function analysis (SFA), which represents a discrete signal or its spectrum as a weighted sum of singularity functions. Through this model, an MR image's low spatial frequency components corrupted by a smoothly varying bias field are first removed, and then reconstructed from its higher spatial frequency components not polluted by bias field. The thus reconstructed image is then used to estimate bias field for final image correction. The approach does not rely on the assumption that anatomical information in MR images occurs at higher spatial frequencies than bias field. The performance of this approach is evaluated using both simulated and real clinical MR images.

In this paper, the current status of cardiac image registration methods is reviewed. The combination of information from multiple cardiac image modalities, such as magnetic resonance imaging, computed tomography, positron emission tomography, single-photon emission computed tomography, and ultrasound, is of increasing interest in the medical community for physiologic understanding and diagnostic purposes. Registration of cardiac images is a more complex problem than brain image registration because the heart is a nonrigid moving organ inside a moving body. Moreover, as compared to the registration of brain images, the heart exhibits much fewer accurate anatomical landmarks. In a clinical context, physicians often mentally integrate image information from different modalities. Automatic registration, based on computer programs, might, however, offer better accuracy and repeatability and save time.

We propose a novel deformable model to assess the deformation of a textured object in an image sequence by simultaneously tracking edge and intensity information. The proposed model is defined as an elastic region with snake-like rigidity constraints at its boundaries. By regularizing the displacement estimation with an elasticity-based constraint, this model is able to assess physically realistic deformations inside a region. By incorporating rigidity constraint at its boundaries, it can also accurately track edges. The numerical implementation of the model is performed using the finite element method. The good behavior of the proposed model is illustrated on synthetic images which simulates the heart contraction in tagged magnetic resonance imaging (MRI). The contour tracking abilities of the model are also illustrated on standard MR images.

We consider the coding of a quadrangular mesh structure generated by a multiresolution deformable quadtree algorithm. Such a structure has been found efficient for region based video coding, but few works deal with the coding of the mesh structure. We propose to use the rules of the mesh generation to significantly reduce the number of bits required for the coding of the nodes position defining the mesh structure. This reduction induces an improvement of either the image quality or either the global bit rate.

Motion and deformation analysis of the myocardium are of utmost interest in cardiac imaging. Part of the, research is devoted to the estimation of the heart function by analysis of the shape changes of the left-ventricular endocardial surface. However, most clinically used shape-based approaches are often two-dimensional (2-D) and based on the analysis of the shape at only two cardiac instants. Three-dimensional (3-D) approaches generally make restrictive hypothesis about the actual endocardium motion to be able to recover a point-to-point correspondence between two surfaces. The present work is a first step toward the automatic spatio-temporal analysis and recognition of deformable surfaces. A curvature-based and easily interpretable description of the surfaces is derived. Based on this description, shape dynamics is first globally estimated through the temporal shape spectra. Second, a regional curvature-based tracking approach is proposed assuming a smooth deformation. It combines geometrical and spatial information in order to analyze a specific endocardial region. These methods are applied both on true 3-D X-ray data and on simulated normal and abnormal left ventricles. The results are coherent and easily interpretable. Shape dynamics estimations and comparisons between deformable object sequences are now possible through these techniques. This promising framework is a suitable tool for a complete regional description of deformable surfaces.

In medical imaging, 3D boundary extraction is a preliminary requisite for a coherent shape analysis of an organ. Deformable objects, like the heart cavities, are often hard to detect because of the artefacts caused by the motion. The authors present a 3D deformable surface model based on a parameterized representation combined with a random process of deformation. The solution is searched for by the minimization of an energy function through simulated annealing. The authors also discuss the introduction of a priori shape information about the object. The boundary extraction algorithm is applied to 3D CT data of a dog's heart.