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Early life and education
Walter Jackson Freeman II was born to Walter Jackson Freeman and his wife, nee Connie Keen. Walter Jackson Freeman was a physician, as was his father-in-law, Walter Williams Keen. Walter Jackson Freeman II was his parents' first child, and he eventually had six siblings. As a child, his family lived in Rittenhouse Square, Philadelphia. Freeman was intelligent, shy, and nonathletic as a child. He had a religious upbringing, but his family was never very close. They regularly gathered for family events at Walter Williams Keen's house. Keen was a distinguished doctor who performed the first American removal of a primary brain tumor and the first colostomy in America. By 1911 Freeman had grown close with his grandfather.

Freeman entered Yale University at 16 years old. He initially experienced social and academic difficulties there. He initially planned to become an engineer, but after contracting typhoid fever, he became interested in medicine, though his father tried to dissuade him from pursuing it. As an upperclassman, he saw more social and academic success. After graduating from Yale in 1916, he took some science classes at the University of Chicago to prepare for medical school. In the fall of 1916 he enrolled in the University of Pennsylvania medical school. Unlike many of his undergraduate classmates, Freeman was exempted from service in World War I because of his enrollment in medical school. He excelled in medical school and became interested in the study of the brain. In medical school, Freeman joined the Medical Enlisted Reserve Corps. In the summer of 1918, he served as an Army doctor in a hospital near Wrightstown, New Jersey, taking the rank of Sergeant. After returning to medical school in late 1918, Freeman took issue with military procedures and was demoted. In his final year of medical school, Freeman found himself drawn to the new specialty of neurology. He graduated second in his class in 1920. He grew distant from his family during his education. His father died in 1920 and he inherited $7,000 from his estate. In 1921 he interned at University Hospital in Pennsylvania. As an intern, he enjoyed studying patients and was fascinated by neuropathology. In his second year as a resident at the hospital, he met Madeline James, and they became romantically involved. Freeman was selected for an American Field Service Scholarship that would fund study in Europe.

France
In 1923, Freeman traveled to the Pitié-Salpêtrière Hospital in Paris, France, to study neurology under Pierre Marie. Freeman was recommended to the institute's faculty by his grandfather. At that time, France was a common destination of American medical students. Freeman kept meticulous notes that documented his experiences in France, later combining them into a single document, which he shared with family and friends. During his studies, he became proficient in French. While studying in Europe, he became disaffected with organized religion.

Initially, Freeman was surprised by the frequency with which Cisterna magna punctures were performed, seeing it as a risky practice. He came to accept the procedure and perform it himself. He later embraced the procedure, referring to it as the "jiffy spinal tap". Freeman was unhappy with the work of general surgeons, which he felt had high mortality rates and was often unsuccessful. Though concerned with the results of surgeons, he was also troubled by patients with brain tumors who were not treated. Neurosurgery was generally not performed in France at that time, but neuroimaging and neurosurgery soon became more common. At the Salpêtrière, Freeman observed the use of lipiodol to treat neuralgia by injection. Freeman soon began to favor early intervention for patients, regardless of the odds of success. He favored making an attempt to treat patients over the focus on observation favored by his colleagues in France. He was also bothered by the lack of laboratory research and experiments. He was able to perform more research on patients than he would have been able to in the US. He also observed patients with psychiatric issues. He described his goal as being the restoration of patients to useful lives. During this time, psychiatrists were taking some ground from neurologists, and the limits of neurology were in flux. Freeman began seeking to reduce neurological issues to being fixable by a one-time procedure.

After completing his studies in France, Freeman traveled to Rome to study neurology at the Clinica Psichiatrica under Giovanni Mingazzini. He learned Italian during his studies there.

Early career
Upon returning to the United States in the summer of 1924, Freeman accepted a job at St. Elizabeth's Hospital in Washington as chief medical officer in charge of laboratories. His grandfather helped him obtain the position. Although he preferred a teaching position, his desired post was not available. He served at the hospital for nine years, during which he gained attention as a promising neurologist. At the hospital, he served under William Alanson White. Freeman oversaw a laboratory of 50 rooms. There he worked alongside Benjamin Karpman. Soon after taking the position, he met Marjorie Franklin, the sister of his brother's college roommate. She worked as an analyst at the US Tariff Commission and had a PhD in Economics. They married in November 1924. They had a daughter in July 1925, twin sons in January 1927, and another son in February 1928. Freeman had two more sons in 1934 and 1936.

By 1930 he had experimented with giving oxygen to mental patients, and even testing it on himself, but found that it did little to remedy catonic states. These experiments were noted in TIME. By this time, he sought organic cures for mental illness and took a dim view of psychoanalysis. He was attracted to the ideas of Adolf Meyer, who said that treating mental illness allowed for society to function smoothly. Freeman then decided to open a private practice in Washington, as well.

Edward Rhodes Stitt, a friend of William Keen, allowed Freeman to gain a position as a lecturer in neuropathology at the U.S. Naval Medical School. He remained in the position for more than ten years. He also served as an associate professor at Georgetown's medical school in an unpaid position for seven years. At Georgetown he performed autopsies for medical patients. He also began teaching neurology at George Washington University. In 1926, he became a full professor and chair of the neurology department there. Georgetown offered him a full professorship as well, but he chose George Washington University. As a young professor, his classes were engaging, and many students came to observe his demonstrations. He also studied pathology at George Washington University, earning a PhD in 1931. He decided to write a textbook neuropathology. Between his writing, academic work, and treatment of patients, he often worked from 4 am until late evening. In 1933, Neuropathology: the Anatomic Foundation of Nervous Diseases was published by W.B Saunders. After concluding the book he had what he described as a "nervous breakdown" and vacationed in France for relief. After his return, he left his position at St. Eliabeth's and began taking barbituates to treat his insomnia. He began focusing more on his private practice. He was a member of several medical societies.

His mother was elected president of the women's auxiliary of the American Medical Association at 64 years old. She died a short time later, leaving Freeman an inheritance that, combined with that he received from his grandfather, insulated him from the effects of the Great Depression.

At George Washington University, Freeman worked to build their neurological laboratory and sought help from those at other institutions. In 1934 he became the secretary of the American Board of Psychiatry and Neurology, serving in that role for 12 years.

In 1931 Freeman traveled to the First International Neurological Congress, where he met Ivan Pavlov. Four years later, at the second conference, he spoke with Egas Moniz. In November 1935, Freeman learned that Moniz had been performing surgery on brains to try to treat mental illness. They corresponded over the next year, and Freeman was impressed by the operations Moniz performed. He resolved to begin doing them himself. Freeman arranged an English publication of writings of Moniz.

In 1935, J. W. Watts began teaching neurosurgery at George Washington University at Freeman's invitation. Freeman convinced Watts of the merits of psychosurgery. After practicing on cadavers, Freeman performed his first leucotomy in September 1936. He viewed it as a success, and soon began photographing patients during procedures. After performing six surgeries that Fall, Freeman contacted Moniz to report his results; Moniz encouraged him to continue. That November, Freeman also spoke with Washington-area reporters and members of the Southern Medical Association about his procedures. Addressing the medical association he touted relief of symptoms, but stopped short of deeming his patients cured. He used the word "lobotomy" to refer to the procedure. Many listeners were skeptical of the procedures, but Meyer was supportive of Freeman and Watts, though he stopped short of endorsing lobotomy. After the conference they had difficulty raising funds but were able to attract more patients. By January 1937 they had performed 20 lobotomies; Freeman viewed most of them successful although one patient died from complications. Freeman led the surgeries though he was not a trained surgeon. After exhibiting at the AMA convention in 1937, they received mass media attention. Psychiatrists were often hostile to lobotomy, and one frequent objection was that the procedure destroyed healthy tissue. In 1939, William Sargant visited the GWU clinic and left with a positive appraisal of their lobotomy practice. In 1941 though, the American Medical Association released a statement critical of lobotomy. In 1937 Freeman and Watts began occasionally performing a second operation on lobotomy patients.

In 1937 Freeman treated several patients with the new treatments of Insulin coma therapy and metrazol, but found them lacking. He began treating patients with electroshock therapy, finding useful for some conditions but inferior to lobotomy in schizophrenic patients.

Beliefs
Freeman was influenced by doctors who taught a localized theory of the functions of the brain, the idea that specific parts of the brain controlled specific functions of the body and they could thus be affected by interventions in that part of the brain, but also by those who saw the brain as a holistic unit and did not believe that specific areas of the brain controlled specific functions. Early in his career, Freeman emphasized the brain's resiliency to critics of the procedure, contrary to what strict believers in localization contended. By the mid-1930s, Freeman had grown frustrated with psychiatry. He believed a physiological cause could be found for mental illnesses and was puzzled by apparently normal brains found in autopsies of schizophrenic patients. He initially suspected that the bodies of mental patients would be abnormal, but after numerous examinations was unable to support this idea.

In 1937, Freeman addressed the Chicago Neurological Society, detailing the results of 20 lobotomies he had performed. He was poorly received; the audience faulted him for proclaiming its effectiveness in the absence of a control group. While the audience was open to the idea of treating mental illness through neurosurgery, they were not convinced that this was the only way and suspected that the placebo affect may have played a role in his results. The next year, along with Watts, he published the results of the lobotomies in the Journal of Nervous and Mental Disease. In the article, he drew no distinction between physical and psychological effects, seeing them both as directly resulting from the surgical actions. Although Freeman's procedures were geared to target a specific function of the brain's anatomy, he evaluated the success of the procedure based on the patient's emotions and behaviors afterwards. He emphasized that success in the procedure allowed the person to function as a whole, without being limited by specific obsessions. He saw mental illness as a preoccupation with parts of the self and normal functions that eventually distracted from the functioning as a whole person. He admitted that patients sometimes lost social capabilities after the procedure but viewed that as a worthwhile sacrifice in his attempts to treat their psychosis, saying "a part of the patient may be sacrificed for the benefit of the whole". Freeman often referenced an address given by Pope Pius XII that asserted that some functions of the body could be sacrificed for the sake of totality; Freeman selectively quoted from the address, leaving out the Pope's strong cautions about medical procedures. He believed that the frontal lobes caused mental illness, though he granted that they were not the only area of the brain that could cause it, so surgical intervention in that area held the possibility to remedy the conditions. He saw treating mental illness as a way to help society as a whole.

Freeman believed that shock therapy would be more effective after lobotomy.