Accurate frequency measurement using PXI 5142 Digitizer

I am Using PXI 5142 Digitizer to read the frequency of a 10 MHz atomic clock up to 8 decimal places. I am using single tone measurement block. But I can't get that accurate fix on the frequency because of the jitter.
Can someone help.
Thanks in Advance.

Thanks For your reply; The device is connected to the digitizer through BNC connector.
Digitzer Scope Settings:  
Samples/seconds --> 2G S/s
Record Length      --> 800
Aqiusition mode   ---> N Samples              
Best Regards,
Helal
Attachments:
Block Diagram.JPG ‏117 KB
Front Panel.JPG ‏91 KB

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