Monte Carlo tomographic reconstruction in SPECT impact of bootstrapping and number of generated events

In Single Photon Emission Computed Tomography (SPECT), 3D images usually reconstructed by performing a set of bidimensional (2D) analytical or iterative reconstructions can also be reconstructed using an iterative reconstruction algorithm involving a 3D projector. Accurate Monte Carlo (MC) simulations modeling all the physical effects that affect the imaging process can be used to estimate this projector. However, the accuracy of the projector is affected by the stochastic nature of MC simulations. In this paper, we study the accuracy of the reconstructed images with respect to the number of simulated histories used to estimate the MC projector. Furthermore, we study the impact of applying the bootstrapping technique when estimating the projectorComment: 15 pages, 9 figures, 2 table

Effect of noise and modeling errors on the reliability of fully 3D Monte Carlo reconstruction in SPECT

We recently demonstrated the value of reconstructing SPECT data with fully 3D Monte Carlo reconstruction (F3DMC), in terms of spatial resolution and quantification. This was shown on a small cubic phantom (64 projections 10 x 10) in some idealistic configurations. The goals of the present study were to assess the effect of noise and modeling errors on the reliability of F3DMC, to propose and evaluate strategies for reducing the noise in the projector, and to demonstrate the feasibility of F3DMC for a dataset with realistic dimensions. A small cubic phantom and a realistic Jaszczak phantom dataset were considered. Projections and projectors for both phantoms were calculated using the Monte Carlo simulation code GATE. Projectors with different statistics were considered and two methods for reducing noise in the projector were investigated: one based on principal component analysis (PCA) and the other consisting in setting small probability values to zero. Energy and spatial shifts in projection sampling with respect to projector sampling were also introduced to test F3DMC in realistic conditions. Experiments with the cubic phantom showed the importance of using simulations with high statistics for calculating the projector, and the value of filtering the projector using a PCA approach. F3DMC was shown to be robust with respect to energy shift and small spatial sampling off-set between the projector and the projections. Images of the Jaszczak phantom were successfully reconstructed and also showed promising results in terms of spatial resolution recovery and quantitative accuracy in small structures. It is concluded that the promising results of F3DMC hold on realistic data set

Reconstruction tri-dimensionnelle complete d'images en spect-ct par modelisation Monte-Carlo

présenté par Z. El Bitar, proceedings sous forme de CDEn tomographie d'émission monophotonique (SPECT), les images 3D normalement reconstruites par des algorithmes de reconstruction analytiques ou itératives bidimensionnelles (2D) pourraient aussi bien être reconstruites avec des algorithmes de reconstruction itérative (3D) qui permettent de compenser les effets physiques perturbant le processus de formation de l'image notamment l'atténuation et la diffusion. Nous avons étudié une technique de reconstruction 3D complète (F3DMC) (Lazaro et al. NIM 2004), dans laquelle le projecteur 3D impliqué dans la reconstruction est estimé par des simulations Monte-Carlo effectuées à partir de données tomodensitométriques du patient

Targeted fully 3D Monte Carlo reconstruction in SPECT

PCSV, présenté par Z. El Bitar, soumis aux proceedingsFully 3D Monte-Carlo (F3DMC) reconstruction consists in calculating a fully 3D object-specific system matrix using Monte-Carlo simulations and inverting it using an iterative approach. To reduce the large amount of disk space required by this approach, we derived a targeted F3DMC approach (TF3DMC) in which the volume to be reconstructed is irregularly sampled, so that pre-identified functional regions of interest are reconstructed using fine sampling while regions with non-specific activity or without any particular interest are coarsely sampled. This method was assessed using simulated and real SPECT data of a phantom filled with Tc99m. The GATE Monte-Carlo simulator was considered to simulate the phantom data and to calculate the system matrices needed for the reconstruction of the simulated and of the real SPECT data. Activity ratios measured in TF3DMC images were compared with those measured on F3DMC and OSEM images corrected for scatter, attenuation and detector response function. TF3DLMC yielded errors less than 10% in activity ratio estimates in hot regions, while errors with quantitative OSEM were between -21% and -3%. The space needed to store the system matrix was divided by a factor from 3.5 to 9.4 compared to F3DMC, for similar or even better accuracy in activity ratio estimates. These results suggest that TF3DMC can be made practical and outperforms F3DMC and OSEM in terms of quantitative accuracy

Les grilles de calcul au service de la physique médicale

présenté par C.O. Thiam, proceedings sous forme de CDLes Simulations Monte Carlo GATE en radiothérapie nécessitent plusieurs heures de calculs. En effet, un résultat précis ne peut être obtenu qu'en générant beaucoup d'événements. Nous étudions donc les capacités des grilles de calcul notamment en terme de réduction des temps de calculs, et les services qu'elles offrent pour une utilisation future en milieu médical. Cette infrastructure, s'inscrit dans le cadre du projet européen EGEE. Ce projet consiste à mutualiser des ressources réparties sur différentes sites afin de pouvoir accéder à de la puissance de calcul, à des données partagées et de bénéficier d'une continuité de service

Monte Carlo Simulation With The GATE Software Using Grid Computing

DémonstrationInternational audienceMonte Carlo simulations needing many replicates to obtain good statistical results can be easily executed in parallel using the "Multiple Replications In Parallel" approach. However, several precautions have to be taken in the generation of the parallel streams of pseudo-random numbers. In this paper, we present the distribution of Monte Carlo simulations performed with the GATE software using local clusters and grid computing. We obtained very convincing results with this large medical application, thanks to the EGEE Grid (Enabling Grid for E-sciencE), achieving in one week computations that could have taken more than 3 years of processing on a single computer. This work has been achieved thanks to a generic object-oriented toolbox called DistMe which we designed to automate this kind of parallelization for Monte Carlo simulations. This toolbox, written in Java is freely available on SourceForge and helped to ensure a rigorous distribution of pseudo-random number streams. It is based on the use of a documented XML format for random numbers generators statuses

Analytical, experimental, and Monte Carlo system response matrix for pinhole SPECT reconstruction

Purpose: To assess the performance of two approaches to the system response matrix (SRM) calculation in pinhole single photon emission computed tomography (SPECT) reconstruction. Methods: Evaluation was performed using experimental data from a low magnification pinhole SPECT system that consisted of a rotating flat detector with a monolithic scintillator crystal. The SRM was computed following two approaches, which were based on Monte Carlo simulations (MC-SRM) and analytical techniques in combination with an experimental characterization (AE-SRM). The spatial response of the system, obtained by using the two approaches, was compared with experimental data. The effect of the MC-SRM and AE-SRM approaches on the reconstructed image was assessed in terms of image contrast, signal-to-noise ratio, image quality, and spatial resolution. To this end, acquisitions were carried out using a hot cylinder phantom (consisting of five fillable rods with diameters of 5, 4, 3, 2, and 1 mm and a uniform cylindrical chamber) and a custom-made Derenzo phantom, with center-to-center distances between adjacent rods of 1.5, 2.0, and 3.0 mm. Results: Good agreement was found for the spatial response of the system between measured data and results derived from MC-SRM and AE-SRM. Only minor differences for point sources at distances smaller than the radius of rotation and large incidence angles were found. Assessment of the effect on the reconstructed image showed a similar contrast for both approaches, with values higher than 0.9 for rod diameters greater than 1 mm and higher than 0.8 for rod diameter of 1 mm. The comparison in terms of image quality showed that all rods in the different sections of a custom-made Derenzo phantom could be distinguished. The spatial resolution (FWHM) was 0.7 mm at iteration 100 using both approaches. The SNR was lower for reconstructed images using MC-SRM than for those reconstructed using AE-SRM, indicating that AE-SRM deals better with the projection noise than MC-SRM. Conclusions: The authors' findings show that both approaches provide good solutions to the problem of calculating the SRM in pinhole SPECT reconstruction. The AE-SRM was faster to create and handle the projection noise better than MC-SRM. Nevertheless, the AE-SRM required a tedious experimental characterization of the intrinsic detector response. Creation of the MC-SRM required longer computation time and handled the projection noise worse than the AE-SRM.Nevertheless, the MC-SRM inherently incorporates extensive modeling of the system and therefore experimental characterization was not required

Aging of the mammalian gastrointestinal tract: a complex organ system

Gastrointestinal disorders are a major cause of morbidity in the elderly population. The gastrointestinal tract is the most complex organ system; its diverse cells perform a range of functions essential to life, not only secretion, digestion, absorption and excretion, but also, very importantly, defence. The gastrointestinal tract acts not only as a barrier to harmful materials and pathogens but also contains the vast number of beneficial bacterial populations that make up the microbiota. Communication between the cells of the gastrointestinal tract and the central nervous and endocrine systems modifies behaviour; the organisms of the microbiota also contribute to this brain–gut–enteric microbiota axis. Age-related physiological changes in the gut are not only common, but also variable, and likely to be influenced by external factors as well as intrinsic aging of the cells involved. The cellular and molecular changes exhibited by the aging gut cells also vary. Aging intestinal smooth muscle cells exhibit a number of changes in the signalling pathways that regulate contraction. There is some evidence for age-associated degeneration of neurons and glia of the enteric nervous system, although enteric neuronal losses are likely not to be nearly as extensive as previously believed. Aging enteric neurons have been shown to exhibit a senescence-associated phenotype. Epithelial stem cells exhibit increased mitochondrial mutation in aging that affects their progeny in the mucosal epithelium. Changes to the microbiota and intestinal immune system during aging are likely to contribute to wider aging of the organism and are increasingly important areas of analysis. How changes of the different cell types of the gut during aging affect the numerous cellular interactions that are essential for normal gut functions will be important areas for future aging research

It’s not the size, it’s the relationship: from ‘small states’ to asymmetry

Debate about the definition of “small state” has produced more fragmentation than consensus, even as the literature has demonstrated its subjects’ roles in joining international organizations propagating norms, executing creative diplomacy, influencing allies, avoiding and joining conflicts, and building peace. However, work on small states has struggled to identify commonalities in these states’ international relations, to cumulate knowledge, or to impact broader IR theory. This paper advocates a changed conceptual and definitional framework. Analysis of “small states” should pivot to examine the dynamics of the asymmetrical relationships in which these states are engaged. Instead of seeking an overall metric for size as the relevant variable—falling victim in a different way Dahl’s “lump-of-power fallacy,” we can recognize the multifaceted, variegated nature of power, whether in war or peacetime