Systems and methods for reconstructing medical images are disclosed. Measurement data, such as sinogram data, is received from an image scanning system. A plurality of masks are applied to corresponding portions of the measurement data to generate a plurality of masked measurement data portions. In some examples, the measurement data is encoded before the plurality of masks are applied. A neural network including a plurality of fully connected layers is applied to the plurality of masked measurement data portions to generate a plurality of image patches. The plurality of image patches are then combined to generate an initial image. In some examples, refinement and scaling operations are applied to the initial image and corresponding attenuation maps to generate a final image. In some examples, the final image is stored in a database. In some examples, the final image is displayed for diagnosis.