‘‘I had the sense that we had this amazing tool,’’ Gerber said. ‘‘An analyst sits with a patient, and over the course of weeks, months, years, the person changes. It’s not just behavioral change. Something changes about the person’s structure — their psychic structure, their character structure. Their personality changes. Every therapist feels confident in that and says they know it when they see it, and every patient who has experienced it says to you: Something shifted inside me. But we don’t know what they mean.’’

While working on his Ph.D., Gerber began a research project that tried to make sense of this mysterious process. He recruited psychoanalysts to fill out an extensive weekly questionnaire, documenting what was happening inside their offices, in as much detail as possible, including patient outcomes. Over the decade it took to complete this study, Gerber saw a pattern in the patients who progressed the most. They didn’t move in a linear way from worse to better, from neurotic to not neurotic, as Gerber had supposed at the outset. Rather, roughly in the middle of their treatment, they went through a period of intense flux, oscillating between extremes of behavior, before they began to improve. Gerber uses a term from chemistry to capture what he saw: ‘‘annealing,’’ the act of heating something so that all its molecules dance around wildly and then slowly cooling it back down so that it assumes a new and more stable state.

‘‘But it also left me with a question,’’ he said. ‘‘Where do you go with this next?’’ He decided to attend medical school and in 1997 enrolled at Harvard. Throughout the 2000s, after he graduated, a spate of brain-­imaging studies was published, demonstrating that a course of psychotherapy — even without medication — had measurable, physical consequences in the brain. Many of those studies used f.M.R.I., which detects changes in blood flow to different brain regions, on the theory that identifying these areas would elucidate where and how the brain carries out its functions. Much of the research was looking specifically at the effects of cognitive-­behavioral therapy, which tends to last an average of 12 to 20 weeks; it focuses on altering particular thoughts and behaviors that are causing distress, rather than — as in psychoanalysis — trying to understand how they’ve come to be and what else might be lurking underneath. In part because C.B.T. is designed to show measurable, observable changes in a relatively short time, it is a natural partner for f.M.R.I. research, which works by taking a kind of before-­and-­after snapshot, looking at which parts of the brain show an increase or decrease in activity after therapy.

A sense of excitement shot through the fields of psychology and psychiatry after these studies, which seemed to offer incontrovertible evidence that psychotherapy changes the brain. But Gerber felt that these imaging studies revealed little about the nature of the changes. One often-­reported finding was that as anxious patients who were undergoing C.B.T. began to feel calmer, activity in their amygdalae — the nutlike structures that are integral to the brain’s fear circuitry — significantly quieted. Yet as Gerber points out, this finding is correlational, saying nothing about the underlying cause that has allowed the patients to get better.

Gerber wanted to do research that would combine psychoanalytic thinking and brain imaging in the hope of getting closer to understanding what was actually going on during therapy. In 2003, he met Bradley Peterson, then a professor of child psychiatry at Columbia, who was on his own mission to test the abstractions of psychoanalytic thinking with brain scanners. In one series of experiments, Peterson was using f.M.R.I. to look at the brain while subjects took part in an assortment of mental exercises relevant to psychoanalytic thinking — including, for example, ‘‘self-­regulation,’’ the process by which we learn, over the course of development, how to deal with our impulses and desires. Peterson’s drive to understand the neurobiological basis of this and other psychoanalytic concepts came, he told me, from his deep conviction that these ideas about the human mind remain invaluable.

It is exceedingly difficult to pull a complex idea from the dense thicket of psychoanalytic theory and turn it into something that can be studied in a lab. After all, it isn’t enough to appear at the brain-­scanning machine with the intention of studying, say, ‘‘self-­regulation’’ — it is first necessary to devise an experiment that distills that concept into something concrete and neatly defined, something that can be measured and tested. One researcher in particular has become well known for her success at this: Susan Andersen, a cognitive and social psychologist who has devoted her career to studying transference, first at the University of California, Santa Barbara, and now at New York University. Andersen has taken an idea that was born in a smoky Viennese consulting room and brought it into the exacting atmosphere of her research labs, where the stories being told are about data, not Dora.