there's been more than a few actual brain studies done with high contrast equipment - you can find them by looking on pubmed
So far, they've confirmed that the brain of a trans person matches the gender they identify with and not their assigned gender in some of the following ways:
the structure of some white matter areas
grey matter regions (some part of the basal ganglia I think)
hypothalamus activation in response to stimulus
cortical thickness
These things will be varied from individual to individual, and they were not present in all subjects, but the total numbers were statistically significant versus a control group of cispeople. Some of the tests were done on MTFs only, while others include both. The white matter differences were seen on a test of FTM subjects.
Another one I read talked about how learning is different from gender to gender, and that transpeople tend to learn the way they identity, even if they were socialized and raised as female I assume as the test subjects were adults, and that was probably not something they controlled for.
