Modulation Transfer Function (MTF) is an important method of describing the performance of an optical system. A consequence of applying Fourier theory to image forming optical systems, MTF describes the contrast in the image of a spatial frequency presented in the scene being viewed.
Spatial frequency is measured in cycles per mm in focal image space, and in cycles per milliradian or other angular unit in afocal spaces. "Cycles" is the correct term for sinusoidal MTF response. The term "line pairs" is often used, but strictly speaking line pairs only applies to bar, as opposed to sinusoidal targets. ZEMAX can compute MTF for both bar and sinusoidal targets. 
The bitmap image analysis window above shows 'good' image quality1 in the section showing the three boys: but how good is good? The contrast ratio in the various line images provides quantitative data on the quality of the image formed. MTF describes the transfer of modulation from the object to the image as a function of spatial frequency and is commonly used to specify lens performance, and as optimization and tolerancing targets during lens design. 
The MTF plot for this lens, above, shows the contrast ratio for any spatial frequency up to the maximum that the lens can support. In this case, we choose to limit the spatial frequencies shown to a maximum of 100 cycles/mm. Also shown for reference is the diffraction limited performance of an aberration-free lens of the same f/#. Once you are familiar with MTF plots, you can assess image quality at a glance.
[1] Note that the apparent image quality is reduced by screen resolution and the compression of the image. The original image as produced by ZEMAX is of photographic quality. See How to Produce Photo-Realistic Output Images for full details.



Many, but not all, optical imaging systems meet the simplifying assumptions necessary for the Fraunhofer diffraction theory used by the FFT MTF algorithm.
The Huygens MTF is not based upon the FFT. The only assumptions are that the the f/# is large enough so that scalar diffraction theory applies and that the sampling is set high enough to accurately model the PSF
You can read more about the Huygens calculation in the article What is a Point Spread Function.
Virtually all imaging systems meet the simplyifying assumptions necessary for computing the Huygens PSF. The Huygens MTF is generally slower than the FFT (Fraunhofer) MTF, but more accurate for those cases where the FFT MTF assumptions do not apply.
There is another case where only the Huygen's calculation can be used: if the chief ray cannot be traced through the system, then a chief-ray centered reference sphere cannot be created. The reference sphere is essential for many wavefront calculations. In this case, the Huygens PSF and MTF calculations can be used. One such case is this multiple mirror telescope, in which the chief ray has no path the the image surface. 
Because the chief ray cannot trace to the image surface, OPD cannot be calculated, and any parameter derived from OPD cannot be calculated:
The Huygens' PSF and MTF calculations work perfectly, as they are not dependent on any one ray used as a reference:

This file is part of the standard ZEMAX distribution, and can be found at {ZEMAXroot}\Samples\Non-sequential\Miscellaneous\Multiple mirror telescope.ZMX.
A final benefit of the Huygen's method is that the MTFs over multiple configurations can be summed. This is also of use in multiple mirror telescopes, but particularly in the case of very long baseline instruments, where the primary mirrors are separated by large distances. In this case it is not desired to use a common entrance pupil, because too few rays hit the primary mirrors to be efficient. In this specific case the Huygens' MTF calculation is uniquely capable.
To optimize or tolerance using Huygens' MTF, use the MTH* operands.