6 research outputs found
Les algorithmes de haute résolution en tomographie d'émission par positrons : développement et accélération sur les cartes graphiques
La tomographie dâĂ©mission par positrons (TEP) est une modalitĂ© dâimagerie molĂ©culaire utilisant des radiotraceurs marquĂ©s par des isotopes Ă©metteurs de positrons permettant de quantifier et de sonder des processus biologiques et physiologiques. Cette modalitĂ© est surtout utilisĂ©e actuellement en oncologie, mais elle est aussi utilisĂ©e de plus en plus en cardiologie, en neurologie et en pharmacologie. En fait, câest une modalitĂ© qui est intrinsĂšquement capable dâoffrir avec une meilleure sensibilitĂ© des informations fonctionnelles sur le mĂ©tabolisme cellulaire. Les limites de cette modalitĂ© sont surtout la faible rĂ©solution spatiale et le manque dâexactitude de la quantification. Par ailleurs, afin de dĂ©passer ces limites qui constituent un obstacle pour Ă©largir le champ des applications cliniques de la TEP, les nouveaux systĂšmes dâacquisition sont Ă©quipĂ©s dâun grand nombre de petits dĂ©tecteurs ayant des meilleures performances de dĂ©tection. La reconstruction de lâimage se fait en utilisant les algorithmes stochastiques itĂ©ratifs mieux adaptĂ©s aux acquisitions Ă faibles statistiques. De ce fait, le temps de reconstruction est devenu trop long pour une utilisation en milieu clinique. Ainsi, pour rĂ©duire ce temps, on les donnĂ©es dâacquisition sont compressĂ©es et des versions accĂ©lĂ©rĂ©es dâalgorithmes stochastiques itĂ©ratifs qui sont gĂ©nĂ©ralement moins exactes sont utilisĂ©es. Les performances amĂ©liorĂ©es par lâaugmentation de nombre des dĂ©tecteurs sont donc limitĂ©es par les contraintes de temps de calcul.
Afin de sortir de cette boucle et permettre lâutilisation des algorithmes de reconstruction robustes, de nombreux travaux ont Ă©tĂ© effectuĂ©s pour accĂ©lĂ©rer ces algorithmes sur les dispositifs GPU (Graphics Processing Units) de calcul haute performance. Dans ce travail, nous avons rejoint cet effort de la communautĂ© scientifique pour dĂ©velopper et introduire en clinique lâutilisation des algorithmes de reconstruction puissants qui amĂ©liorent la rĂ©solution spatiale et lâexactitude de la quantification en TEP.
Nous avons dâabord travaillĂ© sur le dĂ©veloppement des stratĂ©gies pour accĂ©lĂ©rer sur les dispositifs GPU la reconstruction des images TEP Ă partir des donnĂ©es dâacquisition en mode liste. En fait, le mode liste offre de nombreux avantages par rapport Ă la reconstruction Ă partir des sinogrammes, entre autres : il permet dâimplanter facilement et avec prĂ©cision la correction du mouvement et le temps de vol (TOF : Time-Of Flight) pour amĂ©liorer lâexactitude de la quantification. Il permet aussi dâutiliser les fonctions de bases spatio-temporelles pour effectuer la reconstruction 4D afin dâestimer les paramĂštres cinĂ©tiques des mĂ©tabolismes avec exactitude. Cependant, dâune part, lâutilisation de ce mode est trĂšs limitĂ©e en clinique, et dâautre part, il est surtout utilisĂ© pour estimer la valeur normalisĂ©e de captation SUV qui est une grandeur semi-quantitative limitant le caractĂšre fonctionnel de la TEP. Nos contributions sont les suivantes :
- Le dĂ©veloppement dâune nouvelle stratĂ©gie visant Ă accĂ©lĂ©rer sur les dispositifs GPU lâalgorithme 3D LM-OSEM (List Mode Ordered-Subset Expectation-Maximization), y compris le calcul de la matrice de sensibilitĂ© intĂ©grant les facteurs dâattĂ©nuation du patient et les coefficients de normalisation des dĂ©tecteurs. Le temps de calcul obtenu est non seulement compatible avec une utilisation clinique des algorithmes 3D LM-OSEM, mais il permet Ă©galement dâenvisager des reconstructions rapides pour les applications TEP avancĂ©es telles que les Ă©tudes dynamiques en temps rĂ©el et des reconstructions dâimages paramĂ©triques Ă partir des donnĂ©es dâacquisitions directement.
- Le dĂ©veloppement et lâimplantation sur GPU de lâapproche Multigrilles/Multitrames pour accĂ©lĂ©rer lâalgorithme LMEM (List-Mode Expectation-Maximization). Lâobjectif est de dĂ©velopper une nouvelle stratĂ©gie pour accĂ©lĂ©rer lâalgorithme de rĂ©fĂ©rence LMEM qui est un algorithme convergent et puissant, mais qui a lâinconvĂ©nient de converger trĂšs lentement. Les rĂ©sultats obtenus permettent dâentrevoir des reconstructions en temps quasi-rĂ©el que ce soit pour les examens utilisant un grand nombre de donnĂ©es dâacquisition aussi bien que pour les acquisitions dynamiques synchronisĂ©es.
Par ailleurs, en clinique, la quantification est souvent faite Ă partir de donnĂ©es dâacquisition en sinogrammes gĂ©nĂ©ralement compressĂ©s. Mais des travaux antĂ©rieurs ont montrĂ© que cette approche pour accĂ©lĂ©rer la reconstruction diminue lâexactitude de la quantification et dĂ©grade la rĂ©solution spatiale. Pour cette raison, nous avons parallĂ©lisĂ© et implĂ©mentĂ© sur GPU lâalgorithme AW-LOR-OSEM (Attenuation-Weighted Line-of-Response-OSEM) ; une version de lâalgorithme 3D OSEM qui effectue la reconstruction Ă partir de sinogrammes sans compression de donnĂ©es en intĂ©grant les corrections de lâattĂ©nuation et de la normalisation dans les matrices de sensibilitĂ©. Nous avons comparĂ© deux approches dâimplantation : dans la premiĂšre, la matrice systĂšme (MS) est calculĂ©e en temps rĂ©el au cours de la reconstruction, tandis que la seconde implantation utilise une MS prĂ©- calculĂ©e avec une meilleure exactitude. Les rĂ©sultats montrent que la premiĂšre implantation offre une efficacitĂ© de calcul environ deux fois meilleure que celle obtenue dans la deuxiĂšme implantation. Les temps de reconstruction rapportĂ©s sont compatibles avec une utilisation clinique de ces deux stratĂ©gies.Positron emission tomography (PET) is a molecular imaging modality that uses radiotracers labeled with positron emitting isotopes in order to quantify many biological processes. The clinical applications of this modality are largely in oncology, but it has a potential to be a reference exam for many diseases in cardiology, neurology and pharmacology. In fact, it is intrinsically able to offer the functional information of cellular metabolism with a good sensitivity. The principal limitations of this modality are the limited spatial resolution and the limited accuracy of the quantification. To overcome these limits, the recent PET systems use a huge number of small detectors with better performances. The image reconstruction is also done using accurate algorithms such as the iterative stochastic algorithms. But as a consequence, the time of reconstruction becomes too long for a clinical use. So the acquired data are compressed and the accelerated versions of iterative stochastic algorithms which generally are non convergent are used to perform the reconstruction. Consequently, the obtained performance is compromised.
In order to be able to use the complex reconstruction algorithms in clinical applications for the new PET systems, many previous studies were aiming to accelerate these algorithms on GPU devices. Therefore, in this thesis, we joined the effort of researchers for developing and introducing for routine clinical use the accurate reconstruction algorithms that improve the spatial resolution and the accuracy of quantification for PET.
Therefore, we first worked to develop the new strategies for accelerating on GPU devices the reconstruction from list mode acquisition. In fact, this mode offers many advantages over the histogram-mode, such as motion correction, the possibility of using time-of-flight (TOF) information to improve the quantification accuracy, the possibility of using temporal basis functions to perform 4D reconstruction and extract kinetic parameters with better accuracy directly from the acquired data. But, one of the main obstacles that limits the use of list-mode reconstruction approach for routine clinical use is the relatively long reconstruction time. To overcome this obstacle we :
developed a new strategy to accelerate on GPU devices fully 3D list mode ordered-subset expectation-maximization (LM-OSEM) algorithm, including the calculation of the sensitivity matrix that accounts for the patient-specific attenuation and normalisation corrections. The reported reconstruction are not only compatible with a clinical use of 3D LM-OSEM algorithms, but also lets us envision fast reconstructions for advanced PET applications such as real time dynamic studies and parametric image reconstructions.
developed and implemented on GPU a multigrid/multiframe approach of an expectation-maximization algorithm for list-mode acquisitions (MGMF-LMEM). The objective is to develop new strategies to accelerate the reconstruction of gold standard LMEM (list-mode expectation-maximization) algorithm which converges slowly. The GPU-based MGMF-LMEM algorithm processed data at a rate close to one million of events per second per iteration, and permits to perform near real-time reconstructions for large acquisitions or low-count acquisitions such as gated studies.
Moreover, for clinical use, the quantification is often done from acquired data organized in sinograms. This data is generally compressed in order to accelerate reconstruction. But previous works have shown that this approach to accelerate the reconstruction decreases the accuracy of quantification and the spatial resolution. The ordered-subset expectation-maximization (OSEM) is the most used reconstruction algorithm from sinograms in clinic. Thus, we parallelized and implemented the attenuation-weighted line-of-response OSEM (AW-LOR-OSEM) algorithm which allows a PET image reconstruction from sinograms without any data compression and incorporates the attenuation and normalization corrections in the sensitivity matrices as weight factors. We compared two strategies of implementation: in the first, the system matrix (SM) is calculated on the fly during the reconstruction, while the second implementation uses a precalculated SM more accurately. The results show that the computational efficiency is about twice better for the implementation using calculated SM on-the-fly than the implementation using pre-calculated SM, but the reported reconstruction times are compatible with a clinical use for both strategies
Environmental and geochemical characteristics of heavy metals in soils around the former mining area of zeĂŻda (High Moulouya, Morocco)
The ZeĂŻda mining center, closed in the mid-1980s, was once intensively exploited for lead concentrates. Throughout its activity, more than 12 Mt of tailings were generated and, to this day, they are still abandoned in the open air, exposed to weathering conditions without any rehabilitation. The purpose of the present study is to evaluate the environmental and geochemical characteristics of the soils, combining physicochemical, mineralogical, sequential, and kinetic extraction analyses, as well as the metallic spatial distribution and pollution indices of heavy metals (Pb, Cd, Cu, As, and Zn), levels, and risks. The results showed that the abandoned tailings had the highest concentrations of heavy metals, far exceeding their equivalents in the international and local guidelines. The soils spatial distribution maps showed that the levels of heavy metals decreased with distance from the tailings. Based on the pollution indices results, the soils located on and near the tailings are highly contaminated mainly by Pb. While downstream of the tailings, this contamination intensity decreased until becoming null. The sequential extraction results indicated that Pb, Zn, and Cd were primarily associated with the exchangeable fraction in tailings and soils. Therefore, they were more mobile and environmentally hazardous in the study area. The As was mainly associated with the residual fraction, and was thus immobile. Cu was more mobile in tailings as long as it was associated with the reducible fraction while it became immobile in the downstream soils. The kinetic extractions using EDTA and H2O revealed that the labile and less labile fractions were very significant in tailing for the majority of heavy metals. The methodology applied in this study may constitute a valuable tool to develop appropriate mine reclamation solution
Configurations alternatives d'électrodes en tomographie d'impédance électrique génie biomédical
Contamination impact and human health risk in surface soils surrounding the abandoned mine of ZeĂŻda, High Moulouya, Northeastern Morocco
International audienceThe study assesses the levels of 16 heavy metals (HMs) in soils around the Zeida mine to provide information on the extent of contamination, the ecological risk of these HMs in soils, and the health risk to the residents of the Zeida village. Total metal concentrations were determined by inductively coupled plasma-mass spectrometry (ICP-MS) for 20 sampling stations around the mining area. The average concentrations of HMs (mg/kg) in the study area were as follows: Ag (2.3), As (90.4), Ba (1605.1), Be (3.1), Co (11.2), Cr (57.6), Cu (33.9), Mn (499.6), Mo (6.1), Ni (23.4), Pb (1338.7), Sb (7.4), Se (1.3), Sn (11.3), Sr (596.5), and Zn (87.9). They were higher than those at the control sites. Twelve single and integrated ecological risk indices, namely Nemerow Pollution Index (PINemerow), Contamination degree (Cd), and Potential Ecological Risk (RI), were used and suggested that tailings and their nearby soils had a moderate to high contamination potential. Based on the US Environmental Protection Agency (USEPA), the carcinogenic risk, non-carcinogenic, hazard quotient (HQ), and hazard index (HI) were calculated with three routes: ingestion, inhalation, and dermal for children and adults. For both children and adults, HI for HMs was in the order: Mn > As > Co > Pb > 1 > other HMs. Mn, As, and Co were hazardous at 90% of soil sampling stations, while Pb was hazardous in tailings samples. The inhalation and dermal carcinogenic risks presented negligible to acceptable levels. The ingestion carcinogenic risk posed a significant issue for As, which tended to be serious for children at the majority of sampling sites
Accounting for radiation exposure from previous CT exams while deciding on the next exam: What do referring clinicians think?
© 2022 Elsevier B.V.Purpose: To obtain cliniciansâ views of the need to account for radiation exposure from previous CT scans and the advisability of a regulatory mechanism to control the number of CT scans for an individual patient. Methods: A convenience survey was conducted by emailing a link to a three-question electronic survey to clinicians in many countries, mostly through radiology and radiation protection contacts. Results: 505 responses were received from 24 countries. 293 respondents (58%) understand that current regulations do not limit the number of CT scans that can be prescribed for a single patient in a year. When asked whether there should be a regulation to limit the number of CT scans that can be prescribed for a single patient in one year, only a small fraction (143, 28%) answered âNoâ, 182 (36%) answered âMaybeâ and 166 (33%) answered âYesâ. Most respondents (337; 67%) think that radiation risk should form part of the consideration when deciding whether to request a CT exam. A minority (138; 27%) think the decision should be based only on the medical indication for the CT exam. Comparison among the 4 countries (South Korea, Hungary, USA and Canada) with the largest number of respondents indicated wide variations in responses. Conclusions: A majority of the surveyed clinicians consider radiation risk, in addition to clinical factors, when prescribing CT exams. Most respondents are in favor of, or would consider, regulation to control the number of CT scans that could be performed on a patient annually.N
Accounting for radiation exposure from previous CT exams while deciding on the next exam: What do referring clinicians think?
Purpose: To obtain cliniciansâ views of the need to account for radiation exposure from previous CT scans and the advisability of a regulatory mechanism to control the number of CT scans for an individual patient. Methods: A convenience survey was conducted by emailing a link to a three-question electronic survey to clinicians in many countries, mostly through radiology and radiation protection contacts. Results: 505 responses were received from 24 countries. 293 respondents (58%) understand that current regulations do not limit the number of CT scans that can be prescribed for a single patient in a year. When asked whether there should be a regulation to limit the number of CT scans that can be prescribed for a single patient in one year, only a small fraction (143, 28%) answered âNoâ, 182 (36%) answered âMaybeâ and 166 (33%) answered âYesâ. Most respondents (337; 67%) think that radiation risk should form part of the consideration when deciding whether to request a CT exam. A minority (138; 27%) think the decision should be based only on the medical indication for the CT exam. Comparison among the 4 countries (South Korea, Hungary, USA and Canada) with the largest number of respondents indicated wide variations in responses. Conclusions: A majority of the surveyed clinicians consider radiation risk, in addition to clinical factors, when prescribing CT exams. Most respondents are in favor of, or would consider, regulation to control the number of CT scans that could be performed on a patient annually. © 2022 Elsevier B.V