This is one of the most basic measures in adult functional echocardiography. It simply looks at the degree of shortening of the left ventricular diameter between end-diastole and end-systole.
To make the measure use the parasternal long axis view. Place the M mode cursor at the level of the mitral valve tips (so you can see the leaflets flicking in and out of view through the cardiac cycle).
Once the view is obtained measure the end-diastolic diameter (EDD) and end-systolic diameter (ESD). FS = (EDD-ESD)/EDD
As ever this method has some limitations. The left ventricle is often not circular in the newborn period (due to relatively high right ventricular pressure) so assumptions about geometry are not satisfied. In addition it is hard to specify the exact location of the mitral valve tips, and imaging slightly closer to the apex or base of the left ventricle is likely to raise or lower the fractional shortening respectively.