Definitely get 36x6. 12x6 is way too small. Well, I don't know exactly what you need a foam roller for. That would help, but whatever 12x6 can do, 36x6 can do too, and more than that.
I got one this spring for my bursistis. Pretty much "cured" it, but I still keep it in my bedroom in case I need it again. It has lost its "like new" shape after 2 months of daily usage but still worked fine during those flaring-up days.