The NBS Manual would be a good start point to provide some information on experimental designs. 

The manual is downloadable from this site. 

Originally posted by Erfan Naghavi:

Hi Andrew,

Thanks again for your helpful answers—we really appreciate your support!

I have a question about my research idea. I have data from 50 healthy controls and 50 patients. Each person is also classified as either sleepy or not sleepy, giving me two other groups.

I’d like to explore the differences in brain functional connectivity between:

1. Sleepy vs. non-sleepy individuals
   
2. Patients vs. controls within each of those groups
   

I also want to include age, gender, socioeconomic status, and depression as covariates.

Could you please explain how I can set up the contrasts and design matrix efficiently for this kind of analysis?

Thanks again!