I currently work in a government military laboratory (not NIH) and am  interested in getting a PhD. However I want to  remain in the laboratory I currently work in and do my thesis work  there, while being affiliated with a university. My PI is very approving  and encouraging of this and has agreed to serve as a mentor if I find a  program that is willing to accept this.  
Does anyone know if it is possible to be affiliated with a university  but do your thesis work elsewhere? I am specifically looking at schools  in the Washington DC area (JHU, GMU, GWU, GTU, USUHS, etc).