For decades, some doctors have told women that the brain fog, insomnia and mood swings they experience in midlife are “all in their heads.” Now, emerging brain research shows they’re right — but not because women are imagining it.

Brain imaging studies of women - conducted before, during and after menopause - reveal dramatic physical changes in structure, connectivity and energy metabolism. These changes are not only visible on the scans, but many women can also feel them, said Lisa Mosconi, a neuroscientist and author of the book “The Menopause Brain.”

“Menopause does impact the brain,” said Mosconi, an associate professor of neurology and radiology at Weill Cornell Medicine in New York City. “We’re not crazy. We’re not losing our minds.”

Mosconi and her colleagues have been imaging women’s brains and have found that gray matter volume is reduced in areas of the brain involved in attention, concentration, language and memory. There also are changes in connectivity, meaning some areas involved in reproductive functions become less connected, while other regions become more connected. And there are declines in brain energy levels, meaning the brain pulls glucose from the bloodstream and does not burn it as fast or, perhaps, as efficiently as it used to, Mosconi said. Further research is needed, but some of these changes could help explain some of the symptoms of menopause.

And the news is not all bad. For most women, symptoms tend to be temporary and then improve or dissipate after menopause, suggesting that “the brain is adapting to its new biology,” Mosconi said. These “intelligent adaptations,” she said, allow women to live up to a third of their lives after this transition.

“Every time we talk about menopause, it’s always doom and gloom,” she said. “There’s no sense of achievement. There’s no sense of status gained. There’s no sense of having crossed an important milestone. I think that’s absolutely unfair. I’m hoping that we can break the stigma and make menopause an accepted and welcomed part of a woman’s life.”

Estrogen is important for women’s brains, playing roles in regulating behavior, cognitive function and neuronal health. During the menopause transition, which usually starts when women reach their late 30s or early 40s, there is a dramatic drop in estrogen.

In the hypothalamus, which regulates body temperature, dropping estrogen levels can lead to hot flashes. In the hippocampus, which is important for learning and memory consolidation, estrogen loss can affect memory and cognition.

Declining estrogen can disrupt the amygdala, which influences emotional responses; the prefrontal cortex, which is involved in decision-making, attention, multitasking and language; and even the brainstem, which includes some structures regulating sleep-wake cycles, Mosconi said.

Mosconi likened estrogen to an orchestra conductor. “When it withdraws after menopause, the brain keeps going, the orchestra keeps singing, but the tune is not quite the same, and many women can feel the changes.”

Women’s brains evolve throughout their lifetimes — during puberty, pregnancies and the menopause transition, which for many women includes erratic menstrual cycles and an onslaught of hot flashes, night sweats and other symptoms.

The neurons in the brain that were once essential for menstruation and pregnancies are no longer needed, so the brain goes through a “renovation,” Mosconi said.

It is not known whether there is a way to prevent, stop or reverse the changes that occur in the brain during menopause, but at least some of them appear to be temporary. When Mosconi and her colleagues followed up with participants two years later, they found that metabolic activity tends to stabilize in some regions of the brain and that gray matter volume can rebound for some — but not all — women after menopause. More research is needed to better understand when these changes are permanent and when they are temporary, Mosconi said.

Mosconi added that some clinical symptoms of menopause, such as hot flashes, also tend to be temporary, suggesting that the brain has the ability to adapt.

Women’s health experts agree that a combination of a healthy lifestyle and pharmaceutical interventions, when needed, may lead to an easier transition into menopause. In perimenopause, the years leading up to menopause, doctors may prescribe birth control pills to stabilize erratic periods, prevent unwanted pregnancy and ease symptoms, said Sharon Malone, chief medical adviser of Alloy Women’s Health and author of the book “Grown Woman Talk.”

Women who are not experiencing irregular or heavy periods and do not need birth control may opt for menopausal hormone therapy, which uses estrogen or estrogen plus a progestogen to treat hot flashes, night sweats and other symptoms caused by reduced hormone levels.

“Estrogen is not the danger most women think it is,” Malone said. “For the overwhelming majority of women, estrogen can be used safely and effectively. And estrogen is without question the most effective treatment for the symptoms of menopause.”

Overall, the benefits of short-term hormone therapy to treat menopausal symptoms and prevent bone loss have been shown to outweigh the risks for most healthy women, according to a long-term follow-up to the randomized trial called the Women’s Health Initiative, which studied the risks and benefits of hormone use in millions of women.

There is still some question about whether hormone therapy may help with cognition. Age may be a factor. A 2010 study of 5,504 postmenopausal women found that compared with women who were never on hormone therapy, those taking it only in midlife, around age 49, had a 26 percent decreased risk of developing dementia, while those taking it only in late life, about 76, had a 48 percent increased risk.

Aside from medication, diet and nutrition, exercise and sleep have been associated with “a gentler menopause for many women,” Mosconi said. There are also non-hormonal options for treating the symptoms of menopause, including antidepressants, blood pressure medication and anti-seizure drugs.

“There’s a lot of talk about a window of opportunity — that perimenopause should be viewed as a critical window for improving women’s health,” said JoAnn Manson, a professor of medicine at Harvard Medical School and Brigham and Women’s Hospital and a lead investigator on the Women’s Health Initiative.