Hello Lidia,
what you can do in LabVIEW is:
-Use the In Port / Out Port to access shared memory (i.e. to control a sound board)
-Call shared libraries with the Call Library Node
So, in order to achieve what you need, you should ask the embedded PC manufacturer if the register/counter can be accesed by any of those 2 ways (shared memory or through an API/function call).
If you must do it with shared memory, here's a link to those functions for the Linux version of LabVIEW.
http://exchange.ni.com/servlet/ProcessRequest?RHIVEID=101&RNAME=ViewQuestion&HOID=506500000008000000361A0000&ECategory=LabVIEW.LabVIEW+General
Regards,
Jorge