The magnitude and frequency of runout due to vibration of the cage of the spindle motor is detected. A plurality of servo patterns are written to a reference track having a clock pattern on the disc, and the plurality of servo patterns are then read over a plurality of revolutions of the disc using a clock head. The magnitude of position error of the clock head relative to the reference track is identified for each of the read servo patterns. The magnitude and frequency of runout due to cage vibration is identified from the position errors. Servo patterns are written to user tracks on the disc by identifying periods of low magnitude runout due to cage vibration, and writing the servo patterns to the user track during those periods of low magnitude runout.