I want to design a matrix that contains 3 fixed factors. The first is diagnosis (3 levels), the second is gender (2 levels), and the last is imaging site (2 levels). However, the thing is that the imaging site factor only applies to only one level of the diagnosis factor (i.e. patients from the first level of the diagnosis factor were seen in 2 different imaging sites, whereas for the two other groups of patients the same imaging site was used).

I have followed the tutorials but I still be am confused concerning how I should go about creating the design matrix with 3 fixed factors. Would it be:

GroupDescriptorFile 1
Title xx
Class Diagnosis1-Male-Site1
Class Diagnosis1-Female-Site1
Class Diagnosis1-Male-Site2
Class Diagnosis1-Female-Site2
Class Diagnosis2-Male-Site1
Class Diagnosis2-Female-Site1
Class Diagnosis3-Male-Site1
Class Diagnosis3-Female-Site1
Input    etc etc...

Afterwards, if I'm looking for a difference between Diagnosis1 and Diagnosis2, what would be the contrast?
0.25 0.25 0.25 0.25 -0.5 0.5 0 0 ?

Thank you very much for your help,

Shady