OntoVIP: an ontology for the annotation of object models used for medical image simulation

This paper describes the creation of a comprehensive conceptualization of object models used in medical image simulation, suitable for major imaging modalities and simulators. The goal is to create an application ontology that can be used to annotate the models in a repository integrated in the Virtual Imaging Platform (VIP), to facilitate their sharing and reuse. Annotations make the anatomical, physiological and pathophysiological content of the object models explicit. In such an interdisciplinary context we chose to rely on a common integration framework provided by a foundational ontology, that facilitates the consistent integration of the various modules extracted from several existing ontologies, i.e. FMA, PATO, MPATH, RadLex and ChEBI. Emphasis is put on methodology for achieving this extraction and integration. The most salient aspects of the ontology are presented, especially the organization in model layers, as well as its use to browse and query the model repository.

A virtual imaging platform for multi-modality medical image simulation

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.

Optimization of mean-shift scale parameters on the EGEE grid

This paper studies the optimization of Mean-Shift (MS) image filtering scale parameters. A parameter sweep experiment representing 164 days of CPU is performed on the EGEE grid. The mathematical foundations of Mean-Shift and the grid environment used for the deployment are described in details. The experiments and results are then discussed highlighting the efficiency of gradient ascent algorithm for MS parameters optimization and a number of grid observations related to data transfers, reliability, task scheduling, CPU time and usability.

Signal decay due to susceptibility-induced intravoxel dephasing on multiple air-filled cylinders: MRI simulations and experiments

OBJECTIVE

Characterization of magnetic susceptibility artefacts with assessment of the gradient-echo signal decay function of echo time, pixel size, and object geometry in the case of air-filled cylinders embedded in water.

MATERIALS AND METHODS

Experiments were performed with a 0.2 T magnet on a network of small interacting air-filled cylinders along with Magnetic resonance imaging (MRI) simulations integrating intravoxel dephasing. Signal decay over echo time was assessed at different pixel sizes on real and simulated images. The effects of radius, distance between cylinders and main magnetic field were studied using simulation.

RESULTS

Signal loss was greater as echo time or pixel size increased. Voxel signal decay was not exponential but was weighted by sinus cardinalis functions integrating echo time, pixel size and field inhomogeneities which depended on main magnetic field strength and geometric configuration of the object. Simulation was able to model signal decay, even for a complex object constituted of several cylinders. The specific experimental signal modulation we observed was thus reproduced and explained by simulation.

CONCLUSION

The quantitative signal decay approach at 0.2 T can be used in characterization studies in the case of locally regular air/water interfaces as the signal depends on object size relative to pixel size and is relevant to the geometric configuration. Moreover, the good concordance between simulation and experiments should lead to further studies of magnetic susceptibility effects with other objects such as networks of spheres. MRI simulation is thus a potential tool for molecular and porous media imaging.

Measurement of knee cartilage thickness using MRI: a reproducibility study in a meniscectomized guinea pig model of osteoarthritis

The in vivo precision (reproducibility) of quantitative MRI is of particular importance in osteoarthritis (OA) progression of small magnitude and response to therapy. In this study, three-dimensional high-resolution MRI performed at 7 T was used to assess the short-term reproducibility of measurements of mean tibial cartilage thickness in a meniscectomized guinea pig model of OA. MR image acquisition was repeated five times in nine controls (SHAM) and 10 osteoarthritic animals 3 months after meniscectomy (MNX), in vivo. The animals were then killed for histomorphometric assessment and correlation with the MRI-based measurements. Medial tibial cartilage thickness was measured on MR images using semi-automatic dedicated 3D software developed in-house. The reproducibility of measurements of cartilage thickness was assessed by five repeated MRI examinations with a short recovery delay between examinations (48 h). The computed coefficients of variation were 8.9% for the SHAM group and 8.2% for the MNX group. The coefficients of variation were compatible with expected thickness variations between normal and pathological animals. A positive agreement and significant partial correlation (Spearman r' = 0.74; P < 0.01) between the MRI and histomorphometric data was established. Three-dimensional high-resolution MRI is a promising non-invasive research tool for in vivo follow-up. This modality could be used for staging and monitoring therapy response in small-animal models of OA.

Knee cartilage thickness measurements using MRI: a 4(1/2)-month longitudinal study in the meniscectomized guinea pig model of OA

OBJECTIVE

The aim of this study was to follow, over a 4(1/2)-month period, the medial tibia cartilage thickness on a meniscectomy (MNX) guinea pig osteoarthritis (OA) model and to compare with control animals, using three-dimensional high-resolution magnetic resonance imaging (3D HR-MRI).

METHODS

MRI experimentations were performed in vivo at 7 T on guinea pig knee joints. 3D HR-MR images were acquired in 60 controls (SHAM) and 45 osteoarthritic animals (MNX) at four time-points (15, 45, 90 and 135 days) after surgery. Medial tibial cartilage thickness was measured from MRI images using in-house dedicated 3D software followed by a statistical analysis. At each time-point 15 SHAM and 15 MNX animals were sacrificed for histomorphometric assessments.

RESULTS

No significant difference of mean cartilage thickness between the groups was found at early stage (D45) using MRI; however, significant differences were found between the groups at D90 (P<0.001) and D135 (P<0.001). Histomorphometry data confirmed the pathological status of the animals and was well correlated with MRI at D15 (r=0.79, P<0.01), D45 (r=0.67, P<0.01), and D135 (r=0.39, P<0.05) for SHAM, and at D45 (r=0.63, P<0.01), and D135 (r=0.81, P<0.01) for MNX.

CONCLUSION

Medial tibial cartilage measurement based on HR-MR images enables the monitoring of longitudinal cartilage thickness changes. This technique showed significant differences between SHAM and MNX as from D90 after surgery. It could be used as a noninvasive and reproducible tool to monitor therapeutic response in this OA model.

Quantitative study of signal decay due to magnetic susceptibility interfaces: MRI simulations and experiments

Characterization of magnetic susceptibility artifacts is required in a wide range of MRI studies. Experiments with a 0.2T magnet and MRI simulations were used to assess the signal decay over echo time at different pixel sizes in the case of air-water interfaces. The specific experimental signal modulation which was reproduced in simulation was interpreted. Concordance between simulation and experiments should make possible further studies of magnetic susceptibility effects with more complex objects as in molecular imaging and in porous medium imaging.

Magnetic resonance imaging (MRI) simulation on EGEE grid architecture: a web portal design

In this paper, we present a web portal that enables simulation of MRI images on the grid. Such simulations are done using the SIMRI MRI simulator that is implemented on the grid using MPI and the LCG2 middleware. MRI simulations are mainly used to study MRI sequence, and to validate image processing algorithms. As MRI simulation is computationally very expensive, grid technologies appear to be a real added value for the MRI simulation task. Nevertheless the grid access should be simplified to enable final user running MRI simulations. That is why we develop this specific web portal to propose a user friendly interface for MRI simulation on the grid. The web portal is designed using a three layers client/server architecture. Its main component is the process layer part that manages the simulation jobs. This part is mainly based on a java thread that screens a data base of simulation jobs. The thread submits the new jobs to the grid and updates the status of the running jobs. When a job is terminated, the thread sends the simulated image to the user. Through a client web interface, the user can submit new simulation jobs, get a detailed status of the running jobs, have the history of all the terminated jobs as well as their status and corresponding simulated image.

Intensity non-uniformity correction in MRI: existing methods and their validation

Magnetic resonance imaging is a popular and powerful non-invasive imaging technique. Automated analysis has become mandatory to efficiently cope with the large amount of data generated using this modality. However, several artifacts, such as intensity non-uniformity, can degrade the quality of acquired data. Intensity non-uniformity consists in anatomically irrelevant intensity variation throughout data. It can be induced by the choice of the radio-frequency coil, the acquisition pulse sequence and by the nature and geometry of the sample itself. Numerous methods have been proposed to correct this artifact. In this paper, we propose an overview of existing methods. We first sort them according to their location in the acquisition/processing pipeline. Sorting is then refined based on the assumptions those methods rely on. Next, we present the validation protocols used to evaluate these different correction schemes both from a qualitative and a quantitative point of view. Finally, availability and usability of the presented methods is discussed.

The SIMRI project: a versatile and interactive MRI simulator

This paper gives an overview of SIMRI, a new 3D MRI simulator based on the Bloch equation. This simulator proposes an efficient management of the T2* effect, and in a unique simulator integrates most of the simulation features that are offered in different simulators. It takes into account the main static field value and enables realistic simulations of the chemical shift artifact, including off-resonance phenomena. It also simulates the artifacts linked to the static field inhomogeneity like those induced by susceptibility variation within an object. It is implemented in the C language and the MRI sequence programming is done using high level C functions with a simple programming interface. To manage large simulations, the magnetization kernel is implemented in a parallelized way that enables simulation on PC grid architecture. Furthermore, this simulator includes a 1D interactive interface for pedagogic purpose illustrating the magnetization vector motion as well as the MRI contrasts.

Regularized subband coding scheme

Two enhanced subband coding schemes using a regularized image restoration technique are proposed: the first controls the global regularity of the decompressed image; the second extends the first approach at each decomposition level. The quantization scheme incorporates scalar quantization (SQ) and pyramidal lattice vector quantization (VQ) with both optimal bit and quantizer allocation. Experimental results show that both the block effect due to VQ and the quantization noise are significantly reduced.

On the influence of the phase of conjugate quadrature filters in subband image coding

The influence of the phase of conjugate quadrature filters (CQFs) on the performances of a subband coding scheme is analyzed. When the filter length is short, the phase characteristic has virtually no influence on the peak signal-to-noise ratio (PSNR)/bit rate results and on the performance of postprocessing algorithms such as edge detection.