A magnetic resonance (MR) active invasive device system employs a small, high-field polarizing magnet, and a large low-field magnetic resonance (MR) imaging magnet for the purpose of generating MR images of blood perfusion in tissue. A subject is positioned in a large low-field MR imaging magnet. A catheter is inserted into the patient at or near the root of a vessel supplying blood to a portion of tissue to be imaged. A fluid, intended to be used as a contrast agent is first passed through the small high-field polarizing magnet, causing a high degree of net longitudinal magnetization to be produced in the fluid. The fluid is then introduced into the subject through the catheter. Radiofrequency (RF) pulses and magnetic field is gradients are then applied to the patient as in conventional MR imaging. Since the fluid has a larger longitudinal magnetization, before the MR imaging sequence, the fluid produces a much larger MR response signal than other tissue. Images acquired during periods of time in which the fluid is flowing and not flowing are mathematically combined to give an MR image whose pixel intensity is related to the degree of tissue perfusion.