He says confounding factors include neuroplasticity, ignoring the functions of neuroglia, and ordinary small-scale variations that occur:
"the connectome apparently ignores the phenomenon of neuroplasticity.
Plasticity refers to the brain’s ability to physically alter its structure in response to experience. Far from being immalleable, as was once thought, the brain is a highly dynamic organ. Neurons can sprout new connections within minutes of a given stimulus, and entire neural pathways can be rerouted so that function is recovered after a brain injury.
The connectome also disregards the functional importance of neuroglial cells, another class of cells which are found in the nervous system and which outnumber neurons by at least 10 to 1. Once thought to merely provide structural and nutritional support for neurons, glia have, in recent years, come into their own as key players in the brain. As well as performing the roles initially ascribed to them, glia carry out a whole host of other vital functions, including monitoring neuronal health, identifying damaged neurons, and regulating synaptic plasticity. They are also known to be capable of communicating not only with one another, but also with neurons. A map of brain connectivity cannot therefore be complete without taking glia into account.
Finally, although the large-scale connections are very similar among individuals, there are significant variations at smaller scales."