The timebase will not be output via a particular pin. One could possibly probe the timebase pin on the stc, but the stc is confidential information. However, one can still determine if an external or internal timebase is being used.
Go to Measurement and Automation Explorer and open a test panel for your PCI-MIO-16XE-50 card. Select Edge Counting in Counter I/O and then select the appropriate clock. This will count the edges of the selected clock. If you change the external timebase to a slower clock the test panel should account for this, by counting much slower.
