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The continual improvement in spatial resolution of Nuclear Medicine (NM) scanners has made accurate compensation of patient motion increasingly important. A major source of corrupting motion in NM acquisition is due to respiration. Therefore a particle filter (PF) approach has been proposed as a powerful method for motion correction in NM. The probabilistic view of the system in the PF has an advantage in that it considers the complexity and uncertainties of respiratory motion. Tests using the XCAT phantom have previously shown the possibility of estimating unseen organ configurations using training data that only consist of a single respiratory cycle. This paper builds upon previous work in two ways: (i) this is the first evaluation of a PF framework using clinical 4D thoracic CT data; and, (ii) this implementation uses a kernel density estimation (KDE) representation for the transition model, thus taking advantage of the PF's ability to use a wider range of stochastic models. The results show some improvement with the use of a KDE-based transition model and indicates that the PF should be applicable to clinical data.