What is the difference between Asperger disorder and autism? Do doctors know which part of the brain is affected?

Degree of severity. Although there are technical differences for making the diagnosis, in practice, autism is seen as a spectrum disorder. The most severe are diagnosed with autism. Those with the mild symptoms asperger's, and those with symptoms somewhere in between sometimes diagnosed as pdd, nos. The mildest may not diagnosed with anything, but may be thought of as quirky, rigid, or clueless.
Asperger. Asperger is one of disorde known collectively as autism spectrum disorders.