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Low field MRI and MEG are based on the ability of SQUID sensors to detect femtotesla magnetic fields. We are now developing a low field MRI system which can be integrated with the MEG system for small animals. The fast switching of the polarizing field inherently induces large transient signals in low field MRI experiments. We have optimized our system to minimize its influence and to improve the SNR of the MRI signal, by modifying a SQUID gradiometer and FLL (fluxed-locked loop) circuit and by reducing the back electromotive force of the polarizing coil. Our system includes five sets of magnetic field and gradient coils. Employing the “target field method” for the design of shielded planar coils, we achieved the measurement field homogeneity of 0.5% over 40 mm DSV (diameter sphere volume). We observed 4 pT NMR signal from 30 ml water by applying the polarizing field of 4.4 mT and the measurement field of 47 μT (1.9 kHz). The magnetic field noise spectral density is 9 fT/√Hz.