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In ion beam therapy the incidental activation of the irradiated tissue during patient treatment provides a unique opportunity for in-vivo verification. At the Heidelberg Ion Beam Therapy Center (HIT) the post-therapeutical measurement of the irradiation-induced β+-activity, marking the spatial volume of the dose deposition, is planned to be integrated into the clinical workflow to infer valuable information on the correctness of the delivered treatment dose. Currently, a commercial off-line PET/CT scanner and Monte-Carlo methods are under investigation to measure and simulate quantitatively the β+-activity minutes after patient treatment with protons and carbon ions. The comparison of the measured activity with the expected distribution obtained from the simulation, however, requires the following series of dedicated tasks, which are being largely automated through the development of a customized software framework. First, the patient data set is stored anonymously in a separate patient archive (PACS). Affine transformations between the different coordinate systems can be established by a one-time CT-CT registration. Second, the simulation on a properly processed CT is started and monitored on a remote computer cluster. Third, the β+-activity is calculated from the simulated isotope distributions, including time course information and a dedicated model of the biological washout. Finally, measured and simulated activities are visually overlayed to their respective CT volumes for synchronized quantitative analysis. We will present the framework and its application to the analysis of a first patient study with several PET scans acquired few minutes after individual therapy fractions. The comparison with the calculations shows that the beam range can be reliably estimated in bony structures in front of the critical organs, but the modeling of the dynamic washout process has to be improved in soft tissue to allow - ore specific conclusions about the applied treatment dose. Moreover, a second more recent patient study will be addressed, demonstrating the newly developed tools of the framework for a quantitative PET-based in-vivo range assessment.