In this method, you route a pulse of known duration (T) to the Gate of a counter. You can generate the pulse using a second counter. You also can generate the pulse externally and connect it to a PFI terminal. You only need to use one counter if you generate the pulse externally.
Route the signal to measure (fx) to the Source of the counter. Configure the counter for a single pulse-width measurement. If you measure the width of pulse T to be N periods of fx, the frequency of fx is N/T.
The image below illustrates this method. Another option is to measure the width of a known period instead of a known pulse.