All the scientific views on human counciousness and mind transfer are actually very accurate and very well documented...
Just to make an idea how close we are to that read the following articles:
Wikipedia article on mind uploading.
https://en.wikipedia.org/wiki/Mind_uploading
An article on the results of an experiment which consisted to linking a dead rat's brain with a computer. The brain reorganised itself to facilitate communication with the computer (the neuronal clusters were regrouping, adapting). The brain was able to control a simulation running on the computer, which consisted of learning to fly an airplane using 4 directional controls. After continuous trial and error, the rat brain managed to adapt, to actually learn to control the plane inside the simulation. Note that this research was going on in 2004.
http://www.sciencedaily.com/releases/200...104658.htm
http://neural.bme.ufl.edu/page12/page1/page1.html
http://news.discovery.com/tech/robotics/...041022.htm
https://www.youtube.com/watch?app=deskto...w41gH6x_30
A simulated brain (like a scan in the game) is actually being constructed right now, expected to be ready by 2025. They already succesfully simulated simple neural networks like a rat's brain.
https://en.wikipedia.org/wiki/Blue_Brain_Project
http://bluebrain.epfl.ch
Dr. Munshi's research depicted in the beggining of the game, the theory to use a brain scan to similate different treatment plans without risks is already being researched.
http://www.nature.com/news/brain-scan-pr...on-1.13183
http://www.webmd.com/schizophrenia/news/...-treatment
http://psychcentral.com/news/2015/06/26/...86134.html
At a point in the game a scan is refered to as a "Nakajima neurograph". Googling the term came up with a book on brain imaging, and one of the quoted scientific publication on which the book is based was published by a researcher named Nakajima H.
http://www.ncbi.nlm.nih.gov/pubmed/19214684
https://books.google.ro/books?id=vkHVBQA...ph&f=false
The article and book is basically about research in using MRI brain scans to find better treatments for neurological diseases.
This actually proves that the Devs did their homework and went out of their way to create a plausible, credible story!