Udf
how can I define a function (UDF) in cfx? I have a specific thermal function (Pennes equation) for a hemisphere.

I have no idea what Penne equation is. This link tells me it is a heat transfer model used in physiology  http://jap.physiology.org/cgi/content/full/85/1/35  I assume this is what you are talking about.
Looks like you will be able to implement this using source terms on the temperature/heat equation. I don't think you will need fortran. CEL expressions should work fine and they are MUCH easier. 
Cel
thank you for your response.
yeah pennes is a bioheat equation. could you please tell me more about CEL or give me a clue that where I can read about it. thanks 
CFX documentation, reference manual  CEL Expression language.

heat flux
I have simulated a duct with constant walls temperature and air flow inside; how can I get the heat flux from one section of the duct to the other section? or is it possible to get the Nusselt number at one point in fully developed area?

Nusselt number  Yes, define a new variable with an expression with the equation for Nusselt number in CFDPost. Then you can view it, make contours of it and anything else you can do with variables.
Do you mean the heat flux from the air to the wall (look at the wall heat flux variable) or do you mean the heat flux from the convection of the air (make a surface which intersects the flow and define a new variable of density*Cp*normal velocity or something like that.) 
Thank you
actually, I'm looking for hat flux to find the convection coefficient or Nusselt number. if I can define the Nusselt number, there will be no necessity to calculate the heat flux. the problem is I don't know how I can define the Nusselt number. 
As I said, in CFDPost you need to define a new variable which is an equation to define Nusselt number. Then you can view it in CFDPost. Have a look at the CFX tutorials, some of them will define variables in CFDPost for postprocessing.

I already have written the Pennes equation by Fortran, how can I apply it in CFX?

As I said, define a variable in CFDPost and you can get it from there. If you are doing it in the solver then have a look in the CEL reference guide for the list of available variables  you will find wall heat transfer to be useful for you.

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