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If you are using an external clock, then you do not need to export signals at all. You need to bring the clock in on a PFI line and use that PFI line as the timebase for the 50 ms pulse you need to generate.
If you are using the clock of the PXI-6608, put the PXI-6608 in Slot 2 of your chassis. The OCXO clock (which is the 10 MHz clock you need to use for calibration) will automatically overwrite the backplane clock. Then use the DAQmx CIChannel.CounterTimebaseSource Property and set it use the PXI_Clk10_In line.
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Regards,
h_baker
National Instruments
Applications Engineer