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As far as I can tell within an Fourier Transform Spectrometer the spectral information is gained from changing the path length along one arm, this sounds very similar to a michelson interferometer but using two apertures instead of one.

So are there any underlying differences between the two?

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You are right, fourier transform spectrometer is just a scanning Michelson interferometer. In spectroscopic applications these are just synonims. Spectral information is a fourier transform of intensity dependence on path length, thus the name. Usually a term wavemeter is used, meaning some interferometric device to measure wavelength, including FTS as well as Fabry–Pérot interferometers.

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