In May 1991, Dr. Kenneth Kwong, a radiologist at Massachusetts General Hospital, became one of the first scientists to enjoy a new vision of the human brain. The experiment was simple: Kwong would show a subject some visual stimuli - such as a sequence of flashing red lights - and then monitor the brain to see how it reacted. To Kwong's surprise, even a brief light show triggered a telltale pattern of activity in the visual cortex, as the brain processed the sensory information. "It took a few months before I believed what I was seeing," Kwong remembers. "I was actually watching the brain at work." This ability to peer inside the mind was made possible by a new technology known as fMRI, or functional magnetic resonance imaging. The technology quickly became one of the most popular tools of neuroscience. Last year, an average of eight peer-reviewed papers using fMRI were published per day, and more than 19,000 fMRI papers have been published in the last 15 years. The past few months have brought articles on everything from the neural substrate of sarcasm to the patterns of brain activation triggered by pornography. The technique is invading other fields as well, as psychologists, psychiatrists, philosophers, and even economists increasingly rely on these powerful machines. The brain scan image - a silhouette of the skull, highlighted with bright splotches of primary color - has also become a staple of popular culture, a symbol of how scientific advances are changing the way we think about ourselves. For the first time in human history, the black box of the mind has been flung wide open, allowing researchers to search for the cortical source for every flickering thought. The expensive scanners can even decode the hidden urges of the unconscious, revealing those secret feelings that we hide from ourselves. The machine, in other words, knows more about you than you do: It's like a high-tech window into the soul. "These [fMRI] images get people excited in a way that other research just doesn't," says Kelly Joyce, a sociologist at the College of William & Mary. "The pictures have a tremendous authority, not only among scientists but among people who might just glance at a brain scan picture in a newspaper." In recent weeks, however, several high-profile papers have ignited a fierce debate over whether brain scanners are being widely misused and their results over-interpreted. Some eminent figures in the field have taken issue with the metaphors typically used to describe brain imaging, criticizing descriptions of scanners that rely on what Joyce refers to as the "myth of transparency." The scanners, they say, excel at measuring certain types of brain activity, but are also effectively blind when it comes to the detection of more subtle aspects of cognition. As a result, the pictures that seem so precise are often deeply skewed snapshots of mental activity. Furthermore, one of the most common uses of brain scanners - taking a complex psychological phenomenon and pinning it to a particular bit of cortex - is now being criticized as a potentially serious oversimplification of how the brain works. These critics stress the interconnectivity of the brain, noting that virtually every thought and feeling emerges from the crosstalk of different areas spread across the cortex. If fMRI is a window into the soul, these scientists say, then the glass is very, very dirty.

"There are so many bad brain imaging studies, it's hard to believe," says Nikos K. Logothetis, director of the Max Planck Institute for Biological Cybernetics in Germany. "Too many of these experiments are being done by people who, unfortunately, don't really understand what the technology can and cannot do." Logothetis and others believe that much of the misuse stems from the visual nature of the data. One study, by researchers at Colorado State University, showed that simply giving neuroscience students images from an fMRI machine, even if the images were redundant or irrelevant, made the students significantly more likely to find the data credible. According to Paul Bloom, a psychologist at Yale, this is because fMRI "has all the trappings of work with great lab-cred: big, expensive, and potentially dangerous machines, hospitals and medical centers, and a lot of people in white coats." The data looks rigorous - it has the veneer of cutting-edge science - and people assume it's valid, even when the reasoning is shoddy. "You can't just put people in a scanner and ask them whatever question you want," Logothetis says. "Many of these [fMRI] papers are such oversimplifications of what's happening in the brain as to be worthless." A typical fMRI experiment goes like this: a subject is slipped into a tight space that's about the size of a coffin. The person is told to lie perfectly still, as even the slightest movement will muddy the results. At first, the subject does nothing. Then, he or she performs the experimental task, which might involve looking at a picture or making a decision. While this is happening, noisy magnets whir overhead, as the machine detects the slightly different magnetic properties of blood with and without oxygen. The underlying assumption is that more active neurons require more oxygenated blood. Follow the oxygen, and you can construct precise maps of the brain at work. Last year, the New York Times published an op-ed that used fMRI to investigate the brains of swing voters as they stared at photos and videos of presidential candidates. For instance, the scientists found that pictures of Mitt Romney led to activity in the amygdala, while pictures of Hillary Clinton activated the anterior cingulate. (Interestingly, the only two candidates who inspired "little activity in areas of the brain associated with thought or feeling" were Barack Obama and John McCain.) Within days, 17 prominent cognitive neuroscientists signed a letter criticizing the study. "We are distressed," the scientists wrote, "by the publication of research . . . that uses flawed reasoning to draw unfounded conclusions about topics as important as the presidential election." The critics pointed out that a specific brain area, such as the amygdala, can be involved in the production of a wide variety of emotions, from fear to pleasure. This makes it extremely difficult, if not impossible, to decipher the hidden feelings of people based on brain scans alone.