In this study we propose a method to quantify the distribution of Super Paramagnetic Iron Oxide (SPIO) particles with MRI. This task is particularly challenging due to the extreme distortion that these particles produce in the image. Our method is based on a supervised feed-forward deep learning model. The estimation of total quantity of SPIO was in the order of 9% error. This is potentially useful for detecting breast cancer metastasis by identifying residual particles in the breast and eventually other organs.