Fourier domain: temporal versus spatial
I have done very little work using 2-dimensional FFTs.  Most of my work deals with speech, so the short-term Fourier transform applied to a 1-dimensional speech signal is what I understand.

I do not know of a "canned" function, particularly in Matlab, that would realize the time-varying "temporal Fourier domain" characterization that you require.  However, I would suspect you could apply a 2-dimensional FFT to a set of time-slices extracted from the original video sequence that you are working with.  The time resolution of when the slices are extracted would depend on the nature of the events captured by the video.  The magnitude and phase response of each 2-dimensional FFT computation could then be determined and examined to see how the Fourier domain response changes across time.

From what I understand, viewing images in the Fourier domain is not readily intuitive.  I believe the Fourier domain is used to realize efficient image filtering.

I hope this helps.