Magnetic resonance imaging cerebral blood perfusion measurement in awake mice

Cerebral blood perfusion (CBP) plays a vital role in delivering oxygen and essential nutrients to support neuronal activity. Researchers commonly use mouse models with magnetic resonance imaging (MRI) to study CBP and brain function. However, a major challenge in these studies is the use of anesthesia, which significantly alters cerebrovascular dynamics and metabolic activity.

A 3D-printed, custom-designed frame and head mounting plate were used with an existing Bruker mouse cradle. To evaluate the repeatability of CBP measurements in awake versus anesthetized conditions, we used a flow-sensitive alternating inversion recovery (FAIR) sequence on a wild-type mouse that underwent a three-day training before scanning to acclimate it to the MRI environment.

CBP was significantly higher under anesthesia than in the awake condition for both the whole brain and cortex (P < 0.001). Under anesthesia, the mean perfusion for was 70.9 ± 5.6 ml/min/100 g for the whole brain and 67.8 ± 8.5 ml/min/100 g for just the cortex. Under awake conditions, the whole brain perfusion was 51.1 ± 3.3 ml/min/100 g and 46.7 ± 3.4 ml/min/100 g for the cortex. Perfusion variability, measured by variance and standard deviation, was consistently higher under anesthesia.

We built a unique mouse head stabilizing system for MRI and are the first to have specifically focused on CBP during awake conditions.

Our findings confirm that anesthesia significantly increases CBP, affecting the accuracy, reproducibility and relevance of perfusion-related studies. Accordingly, we developed a practical, MRI-compatible setup for imaging awake mice and used it to measure perfusion for more reliable neuroimaging research.