A system and method for imaging a subject includes a first imaging pulse sequence having gradient blips along an x-direction and a y-direction to acquire calibration image data from multiple slices. The imaging pulse sequence also includes a plurality of Z-shimming gradient blips coincident in time with the gradient blips along the x- and y-directions and varied within each slice. A plurality of calibration images are reconstructed from the calibration image data and a comparison image is formed by selecting an image from the calibration images corresponding to at least one of the varied Z-shimming gradient blips for each slice to determine a desired value of the Z-shimming gradient blips. The desired values are used to perform a second pulse sequence to acquire clinical image data from the subject. The second pulse sequence is used to acquire clinical images having been compensated for magnetic susceptibility variations within the subject.