I use FreeRADIUS and MikroTik together. Great team, if you ask me.
The FreeRADIUS setup is standard. Needs no special tweeking for MikroTik. Insure you add the MikroTik box info to your clients.conf file.
The setup in MikroTik is simple. Once you get the hotspot set up and working:
/radius add service=hotspot address=xxx.xxx.xxx.xxx secret=radiussecret
/ip hotspot profile set X use-radius=yes
Change the xxx.xxx.xxx.xxx and radiussecret to your FreeRADIUS server IP and radius secret.
Change the X to the hotspot profile number.