How Brain Mapping Works

By: Susan L. Nasr & Sascha Bos  | 
System of neurons with glowing connections on black background
Neurons transfer information in the human brain, but getting a map of the action takes a while. Andriy Onufriyenko / Getty Images

The human brain is a knot of 100 billion neurons and support cells. We can store a lifetime of memories there. We can use it to write sonnets and build airplanes. Sure, an elephant's brain is larger, weighs more and has more neurons, but elephants also lack our abilities.

Intrigued? Scientists sure are. That's one reason why they are mapping the human brain, a substantial project that could take decades to complete.


Brain mapping attempts to relate the brain's structure to its function, or finding what parts give us certain abilities. For example, what aspect of our brain allows us to be creative or logical? This is called localization of function.

Mapping Functions

In mapping brain functions, scientists use imaging to watch the brain working on various tasks. Charles Wilson, a neurobiologist at the University of Texas at San Antonio, explains localization of function this way:

"There's part of the brain that has to do primarily with vision and other parts that have to do primarily with sound. Now, can we look in the vision section and say, Is there a special part of the brain that detects red objects and another that detects green objects? Or does the same area detect objects of both colors?"

Brain mapping also looks from the outside in. It examines how our environment changes our brain's structure by studying, for instance, how the brain changes physically through the learning and aging processes. Brain mapping also examines what goes wrong physically in the brain during mental illnesses and other brain diseases.


Finally, brain mapping aims to give us a thorough picture of our brain's structure.

Google Earth shows us satellite images of our planet and zooms in to continents, countries, states, cities, highways, streets and buildings. A complete structural map of our brain might be similar.

It could show us our whole brain; all the regions, functional lobes, specialized centers, thick neuron "bundles" connecting brain parts, neuron circuits, single neurons, junctions between neurons and finally, neuron parts. Scientists are still developing the parts that might form this massive map.

Brain mapping uses a collection of many different tools. Researchers must collect images of the brain, turn those images into data, and then use that data to analyze what happens in the brain as it develops.


Brain Mapping Technology and Methods

We've come a long way from this.
Mark Strozier/©

Scientists use both functional and structural neuroimaging in brain mapping research. They take pictures of healthy brains and compare them to diseased brains.

In addition, they examine brains taken from humans, primates and small mammals and try to understand how invertebrates' smaller nervous systems work. On a microscopic level, they also examine neurons.


Here are some tools used in brain mapping. These brain mapping techniques take images of the brain:

  • Computer axial tomography (CAT) scan x-rays the brain from many angles and show structural abnormalities.
  • Structural magnetic resonance imaging (MRI) takes advantage of water in the brain to create images with better resolution than a CAT scan.
  • Diffusion tensor-MRI (DTI) images "tracts" of neurons that connect brain regions by following water movement in the brain.

These techniques examine brain activity:

  • Electroencephalography (EEG) indicates electrically active locations in the brain using detectors implanted in the brain or worn on a cap.
  • Positron emission tomography (PET) takes images of radioactive markers in the brain.
  • Functional MRI (fMRI) shows images of brain activity while subjects work on various tasks.
  • Pharmacological functional MRI (phMRI) shows brain activity as drugs are administered.
  • Transcranial magnetic stimulation (TMS) noninvasively stimulates parts of the brain to trigger certain behaviors.

­New methods allow researchers to see all the connections between neurons in an intact brain. This branch of study is called connectomics. The "wiring diagram" of a brain is called a connectome [source: Lichtman].

"Until recently, we've had no hope of getting these wiring diagrams," says Jeff Lichtman, a Harvard biologist who led the group that developed some of the new techniques. "We could see individual cells, but never all of them at once."

Brainbow labeled the neurons in this transgenic mouse brain with about 90 different color combinations.
Stringer/Getty Images/AFP

One such technique, known as Brainbow, labels every neuron in a live animal's brain a different color. By generating images of the animal's brain, scientists can see where and how neurons connect to each other. As the animal grows and ages, they can also watch how the neurons change connections.

Another technique uses the ATLUM, or automatic tape-collecting lathe ultramicrotome. This machine reads the wiring diagram of a brain.

"We do something akin to paring an apple," explains Lichtman. "We essentially shave off a spiral cut as we rotate the brain on a lathe and put this ribbon of tissue onto a tape. We'll eventually get a hugely long tape, which is essentially the whole brain. Using an electron microscope, we will image that to see the structure of the wiring."

So far, Brainbow and the ATLUM are being used only to study animals with relatively small brains, like mice.

So, what's the point? What, if anything, can mapping accomplish? Explore what we can learn from mapping the human brain in the next section.

Can a phMRI Study Pain?

Since 1997, a group of researchers at Britain's Oxford Centre for Functional Magnetic Resonance Imaging of the Brain have recorded images of patients' brains as they experience pain and various forms of relief including distraction and medication.

By measuring a drug's effect on the brain, scientists have been able to learn more about analgesic and psychiatric drugs.


Uses of Brain Mapping

Why would scientists take on the arduous task of brain mapping? The answer is simple, says Lichtman: to understand our brains more intimately.

We have never seen a diagram of how all of the neurons in the brain connect. As Jeff Lichtman puts it, "A lot of our thinking about the brain is based on incomplete knowledge of what is actually there. So we would like to see what is actually there."


The brain's wiring diagram may help us better understand how we learn and adapt, says Lichtman:

"We start out being less well-adapted to our environment than any other animal. By the time we're adults, we can use tools that our genetic heritage couldn't possibly have taught our nervous system to use — like iPods. No other animal can do that. During our development, we must wire ourselves to [be able to] use these machines."

Brain mapping is also of practical use to doctors. Neurosurgeons use brain mapping to plan safer surgeries. One treatment for epilepsy, for example, removes the affected part of the brain.

Using functional MRI and EEG, surgeons can locate the seizure center in a patient's brain — as well as areas that are active during speaking and moving — down to the millimeter. These images tell doctors what to leave and what to cut out.

Brain imaging is not only used in treatment. It is used to diagnose neurodegenerative diseases like Parkinson's and Alzheimer's [source: Wilson]. Using tagging techniques like PET, doctors look for drops in certain brain chemicals, or they may use MRI to examine shrinkages in areas show tissue loss.

Over time, doctors can map what the brain looks like as diseases progress or as treatments work [source: Institute for Neurodegenerative Disorders].

Developmental disorders like autism may have a structural basis in the brain. Lichtman points out that autism is thought to involve a series of unique connections between neurons. By applying Brainbow to a mouse with autism, researchers might see the wiring diagram evolve to find out how, when and if the wiring differs from a mouse without autism.

Scientists have also sought to illustrate the effects of various psychiatric disorders in the brain, with some success. Brain imaging on these patients revealed structural abnormalities. For example, structural MRI has shown that schizophrenic patients lose matter in the temporal and prefrontal cortex over time [Source: Thompson et al.].

Panic disorder, bipolar disorder, depression, anxiety, eating disorders and more are being examined using different brain imaging techniques, but how do we interpret scientists' findings? More importantly, where can we see them?

Doctors and scientists have learned more from brain mapping than this article can cover. Here are two highlights:


We detect sarcasm using a brain region called the right parahippocampal gyrus. Researchers discovered this using functional MRI on patients with deterioration in that region and have lost all sense of sarcasm [source: Hurley].


According to Rodolfo Llinas of New York University, we can divide the brain into a synchronization center deep in the brain and neuron loops that give us higher thought.

We feel conscious when the center keeps the loops working in harmony. But if either part is damaged, we may lose some or all consciousness, says Nicholas Schiff at Cornell University's Weill Medical College.

This may explain why patients with no outward signs of consciousness for years may show completely normal brain activity in response to a familiar voice. They have loops working in isolation, like the neural networks that process language [source: Zimmer].


The Brain Atlas: How We Use Brain Maps

Microsoft cofounder Paul G. Allen touts the completion of the Allen Brain Atlas on Capitol Hill in September 2006. The project studies the expression of genes in mouse brains.
Mark Wilson/Getty Images News

Neuroinformatics places all the data we have on the brain on the internet in usable form. The data include images, models of neuron behavior and maps of the genes that are "turned on" in different brain regions.

By making the data sharable and searchable, brain researchers can piggyback off of one another's studies and discover more.


Engineers are writing software to help brain researchers share and compare data. Software now analyzes, for instance, whether MRIs of Alzheimer's patients with different brain sizes and shapes have similar brain features.

Are people with a certain brain architecture predisposed to bipolar disorder? This question, and many others, may one day be answered by computer programs that reanalyze images of past patients rather than by studying new ones.

Here are examples of brain atlases that researchers can mine for answers:

  • Allen Mouse Brain Atlas: The mouse brain expresses 21,000 genes. Researchers sliced up the brain and stained where each gene is expressed. Visitors can look at photos or 3-D models of the brain for their gene of interest.
  • Allen Brain Map: Our cerebral cortex allows us to think, reason and remember. Researchers have sliced this up as well. They have also stained where 1,000 genes — and counting — are expressed [Source: Allen Brain Map].
  • Whole Brain Atlas: Stores images of the human brain as it ages and fights diseases [source: Becker].

Images aren't the only source of information. Here are examples of databases brain researchers use:

  • NeuronDB provides diagrams of specific neurons in the human brain and tells you what inputs cause them to fire.
  • ModelDB stores mathematical models of how neurons and neuron networks send electrical signals. "The collection of millions of cells doing that becomes movement, sensation, cognition, emotion and human experience," says Wilson. "To make a model of the brain's function, we start with that."


The Complete Brain Map

A woman examines an exhibit in Dresden, Germany, showing the neurobiological processes of the human brain. Could we eventually map emotions like happiness?
Norbert Millauer/DDP

After imaging the brains of populations large enough to generate statistics, researchers have made sophisticated brain maps. There are maps to illustrate where we lose brain volume as we age, as AIDS progresses and as we use methamphetamines.

What would a complete map of the human brain look like? That depends on your interests. If you thirst to know the brain's structure, you might want to see that hypothetical Google Earth version that can begin with a picture of our cortex and zoom in to neuron number 888,898,432,857.


This complete, Google Earth–type of map is stalled at many points. One such point is the imaging of all of the human brain's neurons and their connections. Even getting this data in the mouse is painstaking, says Harvard biologist Jeff Lichtman.

Mapping the Fruit Fly Brain

For many years, scientists were only able to produce complete maps of interconnecting neurons for species with very simple "brains" consisting of only several hundred neurons. The first of these was Caenorhabditis elegans, "a worm that's a millimeter long and has 300 nerve cells," says Lichtman.

In March 2023, researchers released the first connectome of a complex brain, that of a larval fruit fly (Drosophila melanogaster). Fruit fly brains may seem simple until you realize they have 3,000 neurons and half a million synapses. Mapping the fruit fly brain took over five years.

A Complete Map of the Human Brain

Your definition of a complete brain map depends on your interests. If you're a neuropsychiatrist, for example, a complete map of the brain might be a time-lapse image showing how bipolar disorder unfolds in the brain from birth to the first symptom and what lithium does to stop the process.

That might not be enough for you. You might want to know the function of the brain's every last inch. Unfortunately, that may be impossible. We can't capture functions that happen too quickly or too slowly, says neurobiologist Charles Wilson.

Other processes take a lifetime. No imaging study has followed someone from birth to death. "No method that we know of handles every time of interest. No method we know of handles more than a tiny piece of it," says Wilson. At this point, Lichtman says there is no current effort underway to integrate all of these maps into one.

But there's no fundamental reason why we can't eventually have any — or all — of these maps, says Wilson:

"The problems are all practical technology problems that can be overcome. As with any map, if you start with a crude map, it's better than no map. And you don't need a new map. You just add information to the old map to make it more refined. We aren't going to wake up one day and have this. We are going to add a little today, a little tomorrow, and at some point, we are going to say, 'Wow, this is starting to look pretty good.'"
You Use It All

It is a myth that we use only 10 percent of our brains. We use it all. Brain images have collectively documented activity in all parts. What's more, damage to a small area can wipe out major abilities. Read more about the 10 percent brain myth on professor Eric Chudler's website at the University of Washington.


Lots More Information

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