Greetings,
As it says in the user manual for the PCI-6036E, any PFI line can input the CONVERT or STARTSCAN signals. AI Clock Config is the VI you will use to assign these signals to PFI lines. Two of the examples installed with LabVIEW demonstrate the use of AI Clock Config to configure an external Channel Clock (CONVERT) or Scan Clock (STARTSCAN).
Acquire N Scans - ExtChanClk.vi
Acquire N Scans - ExtScanClk.vi
The documentation for these examples provides detailed information regarding their use.
Good luck with your application.
Spencer S.