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You are seeing that nothing can screw up a perfectly good theory faster than reality. The theory is that a wavefront analysis will provide an accurate prescription. The reality is not quite so simple. You would notice a 0.50 diopter difference.
The manifest refraction (which is better, one or two) is subjective. Based upon your perception of which is better, you are defining your prescription. The WaveScan prescription is objective. Your preferences are not considered as the device reads only the optics of your eye.
The brain is very good at taking inferior optics and interpreting the information into good vision. Throughout your life your brain has learned to “ignore” bad optics and take advantage of good optics. An example of this process is the blind spot. You have a very large blind spot where the optic nerve enters the eye and attaches to the retina. You don’t “see” the blind spot because y our brain has learned how to ignore it and “look around” it.
The wavefront analysis would evaluate the optics of the blind spot and say you have excellent vision at that area, yet you are in-fact without any vision at that area. It would also include the optics of the area in its analysis and proposed treatment plan.
You may also have floaters. These tiny bits of material floating around in your eye tend to be ignored by the brain, but may cause a different reading in a wavefront analysis.
Then there is personal preference. It may be that your preferred prescription- what your brain likes - is not equal to actual optics, but your subject preference makes the difference.
It can also be because of the limitations of the wavefront technology. If there is an aberration in the optics, the wavefront may convert that in a manner that changes the prescription. Each aberrometer has its little quirks. That is why doctors make minor adjustments to future treatment plans as they evaluate past real-world results.
The (very) general rule of thumb is that if the wavefront analysis and the manifest refraction are 1.00 diopter off, use the manifest refraction and set the laser to conventional mode. Your differences are less than 1.00 diopter, so wavefront driven ablation is likely going to be recommended, however your surgeon may make a minor modification in the treatment plan to accommodate for the difference. It is not uncommon for a wavefront created prescription to be different that manifest prescription. If you use an autorefractor, you would probably get a third prescription. This is why having a good surgeon is so important. You need someone who knows how to properly interpret this seemingly conflicting information to provide you the best possible result.