Can't shake this feeling

You know how sometimes your heart tells you one thing and your brain tells you another? Maybe that is just me but I really hate the confusion it brings. The rational mind says this is the right thing to do. The emotional side tells you it sucks. Who do you listen to? I have recently been part of that decision making process. It was largely dictated by the rational side while coming to some sort of resolution. Now, I just cant shake this nagging feeling that I made the wrong decision. I just doesn't feel right. Somehow I listened to the wrong part of me and made the "right" choice. That it is best for everyone involved, but only strictly on a intellectual level.