Tommy,
This can be a bit of work, and is basically what is called Rotoscoping.
It is easier in Adobe Photoshop (either an earlier version of PS Extended, or CS 6), or Adobe After Effects, and especially CS5, or later.
Still, with a bit of work, let's see if we can help you out a bit.
One can create "synthetic" pupils with either a program, like Photoshop, or PsElements, or maybe even with the PrE Titler. I will step you through how I would approach this in Titler. The pupils will be black Filled "circles," which are Shapes. They will be created one per Title, and let's call the one for the left pupil "Left," and the one for the right pupil "Right." With the CTI (Current Time Indicator) over the first Frame of your Video, where you need these "pupils," go to Text>New Text>Default Text (in PrE 11). This will bring up a pretty clean Title, but you will have "Add Text," in it. With the Selection Tool in Titler (arrow), click on "Add Text," to Select it, then Delete it. Now, go to the Shapes Tab, and choose Elipse. Hold down Shift+Alt, then click+drag to create a "circle" centered where you want that circle, i.e. centered on your left eye's pupil, and sized to about that of your pupil. That will draw a white circle. Now, go to the Selection Tool, if your white circle is not still Selected, click on it, then go to the "artist's palette," click on it, and choose black, or very dark gray.
Repeat the above for the left pupil, on a different Title. The reason we are doing in one pupil at a time, is that if you head turns a bit, the distance between those pupils will change, and if you have both circles on one Title, you will be hard-pressed to change that distance, or a variation in height between your two pupils.
At this point, you might want to add a bit of Effect>Blur>Gaussian Blur, so as to not have hard-edged circles for pupils - experiment until you think that it looks pretty natural.
The trick, and the work, will come next. As your created your Left Title, and Right Title over the first Frame of your video, the Position will be perfect. As the Frames of your video progress, they will very likely no longer be in the correct position. You will then need to step through a couple of Frames, and monitor the Position of your Left & Right Titles. When you see that your face has moved, and the Position is not correct, in Applied Effects, Motion>Position, add a Keyframe, and move the Position (this is done separately for each Title), until they match. Repeat - match, repeat - match, repeat - match, until done.
If the "pupils" look a bit too dark and stark, two tricks might be helpful:
- First, experiment with the Opacity Effect of each Title. I am guessing that an Opacity of about 60 - 70% might look a bit better.
- Back in each Title, if it's not too small a working area, think about adding a "catch light" reflection in each of your circles. I would think that a Square Shape, atop the black circle with a medium light gray, might work well. If you did add that Gaussian Blur, then the "catch light" should be slightly Blurred too, and this should work out well.
Now, in Photoshop Extended, or CS 6, you can Import your Video, and then use the Clone Stamp Tool (maybe even Cloning from an actual shot of eyes, with pupils, that you would like), to add the colored pupil. Pretty much the same thing in After Effects, but with the benefit of Motion Tracking, that will likely save a bunch of Keyframing.
One of the limitations of using PrE's Titler, is that one cannot Zoom In, to work very critically. This is a biggie for such fine work, IMO. In both Photoshop, and After Effects, you can Zoom WAY In, to work on tiny Objects.
Good luck, and please let us know how this exercise turns out. Be patient, and prepared to experiment with aspects like the Opacity of the Titles (the pupil circles), and also the Keyframes to keep those over your eyes.
Hunt