In the context of experimental PET imaging, continuously arterial blood sampling is often performed to obtain a time-continuous description of the radiotracer blood activity following its administration. This information is important to quantify the delivery of the tracer into tissues through the kinetic modelling analysis. With the introduction of simultaneous PET-MRI scanners, a new generation of automatic blood samplers compatible with the high magnetic field of the equipment has been introduced; however, the signal-to-noise ratio (SNR) of these counters is much poorer. In this work we extend an existing pipeline of blood modelling (called “MultiBlood”) to the analysis of arterial blood data obtained from MR-compatible samplers. We show that this method can filter out the excess of noise and return blood data time-activity courses comparable with the previous generation of blood samplers.