At first cycle jitter seems easy to compute. Just subtract the average period from each cycle period. But from Cypress Semiconductor application note AN5054, "Understanding Data Sheet Jitter Specifications for Cypress Timing Products":
In accordance with JEDEC standard JESD65B, period jitter
is defined as the deviation in cycle time of a signal with
respect to the average period over a random sample of
cycles.
Note the random sample of cycles. If all consecutive cycles are used, some of the error in one cycle would show up as an opposite error in the next cycle. While peak jitter values would not be affected, distributions would be. This is demonstrated later on.
At this point, only quantization error are being considered. With reference to the above figure,
period_jitter=(t_cycle[n]-cycle_average) for n=1,3,5,...
As well, the cycle average used in these calculations will be the computed value from the digitized data.