Hi,
You have to bring the external reference clock to the SOURCE of the CTR channel, then select the CTR source channel the default one.
The SOURCE pins for CTR0 to CTR7 are PFI 11, PFI 15, PFI 19, PFI 23, PFI 27, PFI 31, PFI 35, PFI 39.
Best regards.
Silvius Iancu