A system for performing magnetic resonance imaging (MRI) of a subject has a pulse sequence system that generates a pulse sequence and has a gradient system, a plurality of gradient coils, a radio-frequency system, and a plurality of RF coils. The pulse sequence system causes the subject to emit MR signals which are captured as k-space data. The system also has a k-space ordering processor that collects first k-space data and second k-space data, an MR signal modeler that generates a signal variation model, and a compensation module that applies the signal variation model to the second k-space data collected to produce compensated k-space data. A display processor reconstructs the compensated k-space data into an image of the subject. The compensated data accounts for variation in magnetization during the pulse sequence and k-space data collection to reduce artifacts in the images.