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In this paper magnetic resonance imaging (MRI) is investigated for monitoring the penetration of high intensity focused ultrasound (HIFU) ex vivo and in vivo rabbit brain. A single element spherically focused transducer of 5 cm diameter, focusing at 10 cm and operating at 2 MHz was used. A prototype MRI- compatible positioning device is described. MRI images were taken using fast spin echo (FSE). The length of the lesions in vivo rabbit brain was much higher than the length ex vivo, proving that the penetration in the ex vivo brain is limited by reflection due to trapped bubbles in the blood vessels.