There are of course brain impairments that cause mental symptoms. These can primarily be divided into acute and chronic presentations. Acute conditions present with a toxic confusional state or delirium, for example related to the general effects of disease in the body. Chronic irreversible conditions are dementia, such as Alzheimer's disease. Such organic presentations can be differentiated on clinical examination of the mental state, as they have cognitive symptoms and signs affecting intellectual functioning, such as orientation (time, place, person), concentration, attention, memory and level of consciousness. These cognitive abnormalities tend not to be present with functional disorders.
Mental disorders are of course mediated through the brain, but it is a conceptual mistake to regard non-organic disorders as being in the brain. People become mentally ill, not their brains. Functional mental disorder needs to be understood in the context of life, social, family and personal development and current situation. It may not be possible to 'prove' what causes mental illness, and it may be very difficult to make sense of some presentations, such as psychosis, but nonetheless any treatment needs to focus on providing the support and understanding to help people recover from their difficulties as much as they are able and wish to do so.