Arterial spin labeling is a versatile perfusion quantification methodology, which has the potential to provide accurate characterization of cerebral blood flow (CBF) in mouse models. However, a paucity of physiological data needed for accurate modeling, more stringent requirements for gradient performance, and strong artifacts introduced by magnetization transfer present special challenges for accurate CBF mapping in the mouse. This article describes robust mapping of CBF over three-dimensional brain regions using amplitude-modulated continuous arterial spin labeling. To provide physiological data for CBF modeling, the carotid artery blood velocity distribution was characterized using pulsed-wave Doppler ultrasound. These blood velocity measurements were used in simulations that optimize inversion efficiency for parameters meeting MRI gradient duty cycle constraints. A rapid slice positioning algorithm was developed and evaluated to provide accurate positioning of the labeling plane. To account for enhancement of T(1) due to magnetization transfer, a binary spin bath model of magnetization transfer was used to provide a more accurate estimate of CBF. Finally, a study of CBF was conducted on 10 mice with findings of highly reproducible inversion efficiency (mean ± standard-error-of-the-mean, 0.67 ± 0.03), statistically significant variation in CBF over 12 brain regions (P < 0.0001) and a mean ± standard-error-of-the-mean whole brain CBF of 219 ± 6 mL/100 g/min.
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