6.2: Imaging brain activity

The earliest methods of analyzing nervous system anatomy were crude: manual dissection of the brain post-mortem (after death). In the 1860s, these methods received attention clinically with the studies conducted by French neurologist and surgeon Paul Broca. One of Broca’s patients, nicknamed “Patient Tan,” had severe language deficits and was only able to say “tan.” Broca performed an autopsy after Patient Tan died, and observed a very localized injury in his brain that was likely the cause of Tan’s language deficits.

At the same time, a pseudoscientific fad was gaining in popularity. Franz Gall, a German neuroanatomist, published a treatise describing phrenology, the belief that we can predict personality traits based on the shape of a person’s head and the bumps on the outside of the skull. According to Gall, behaviors such as romanticism, individuality, and cautiousness are a result of differences in brain anatomy that push the skull outwards.

Today, we know that phrenology is a fad unsupported by the rigorous methodology of science. But there was a valuable lesson that emerged from phrenology which still persists in part today. Both phrenology and Broca’s observation support localization of function, the idea that specific areas of the brain are important for certain functions. Today, we also think about the connections between two areas as being important for healthy brain activity. The techniques discussed below were developed to allow scientists to see some aspect of the anatomy of the nervous system, either gross anatomical differences or connectivity.

Figure 6.6 Drawing of Patient Tan’s brain after Broca’s autopsy (top). Tan’s language disorder was likely a result of the highly localized damage to a region of his left hemisphere. Chart showing the localization of different behaviors according to the pseudoscience practice of phrenology (bottom).

6.1.1 Computerized tomography scan (CT scan or CAT scan)

Example questions answered:

“Does the patient have a brain tumor, and where

is the brain tumor located?”

“Are the meninges intact?”

The CT scan relies on X-ray technology that was developed in 1895. X-rays are high energy beams of electromagnetic radiation that are capable of passing through many physical objects. Traditional two-dimensional X-rays, such as those used to image a broken bone or tooth decay, use radiographic film to detect where the X-rays get blocked. When an X-ray passes unimpeded, it causes the film to darken. But, wherever the X-rays are blocked, the film remains white. Therefore, material that is more dense (such as bone) appears as white, less dense material (such as the air surrounding the body or CSF) appears dark. Other tissue are some shade of gray in between.

Figure 6.7 In X-ray images, dense materials (bone) appear as brighter while less dense smaterials (air) appear as black.

The CT scan is essentially a threedimensional X-ray that revolves around the person as they move through the scanner. Instead of using radiographic film, the CT scan uses a computer that detects the passage of X-rays, located directly across the emission source of the X-ray. Instead of a flat, two dimensional-image, the CT scan uses an X-ray gun that revolves around the person’s body as they advance slowly through a large circular hole. The computer is then able to compile the series of two-dimensional images and turn them into a three dimensional reconstruction that can be used to see the brain from any projection. CT scans give us a spatial resolution of about 0.5 mm. CT scans are generally used clinically to assess diagnostic changes over several days (such as before and after tumor removal or to determine if an intracranial bleed has healed), so temporal resolution is not a major consideration.

Figure 6.8 The patient lies on a table that moves through the middle of the CT scanner.

As an anatomical analysis that can easily identify tissues of different density, it is great for identifying and diagnosing particular brain conditions. Brain tumors can be visualized in a CT scan, since they are identified by an increase in tissue density compared to normal brain tissue. Hydrocephalus, an abnormal and potentially deadly expansion of the CSF-filled ventricles, can be quickly identified by this analysis. Meningitis, an inflammation of the meninges, may present as increased contrast in the CT scan.

The big advantage of the CT scan is that it is noninvasive. You can use a CT scan in order to diagnose and identify the cause of a condition while a person is still alive, and hopefully work towards developing an intervention.

It is also a relatively quick technique. A full head CT scan takes only minutes, which allows for a rapid diagnosis of anatomical structures.

Figure 6.9 What do you notice that is abnormal in this CT scan?

However, X-rays are highly mutagenic. Prolonged exposure to X-rays dramatically increases the risk of developing various cancers, since X-rays interfere with the process of DNA replication. It is estimated that the radiation exposure in a single head CT scan is similar to the background exposure of X-rays in a few months. When a CT scan is prescribed, the diagnostic information gained from a CT scan is more important than the risks from increased radiation exposure.

6.1.2 Diffusion tensor imaging (DTI)

Example questions answered:

“Is the volume of the white matter tract medial longitudinal fasciculus important for normal language processing?”

“Does spinal cord compression cause neurological deficits?”

While a CT scan is great for detecting gross anatomical anomalies like tumors or intracranial bleeding, it has a difficult time with subtle anatomical changes like differences between gray matter and white matter tracts. A technique for identifying these differences was proposed in 1994, called diffusion tensor imaging (DTI).

DTI quantifies white matter because of the morphological features of white matter. More specifically, DTI uses MRI technology (see section 6.2.3 for more information) to detect and quantify the movement of water molecules, which moves differently in gray matter than white matter. A single molecule of water in the middle of a cup can move in any direction with equal probability. This type of motion is called isotropic diffusion. However, the movement of a water molecule in biological tissue is not completely random, largely because the brain is made up of heterogeneous tissue. White matter is very different from gray matter. A water molecule is more easily able to diffuse along the same direction as a tract of white matter, but has a difficult time moving perpendicularly across such tissue. The difference in molecular motion is called anisotropic diffusion. DTI uses the premise that anisotropic diffusion is observed in white matter tracts.

Figure 6.10 Diffusion tensor imaging can be used to visualize tracts of white matter, indicated by different colors.

DTI can give spatial resolution on the order of millimeters. It is generally not used for monitoring changes over time, so temporal resolution is not a major consideration.

Axonal projections are directional, with the soma at one end and the axon terminal at the other. One of the shortcomings of DTI is that it cannot give us information about the directionality of the axonal projections.

Figure 6.11 In isotropic diffusion (top), a single particle is able to move in any direction randomly. However, in anisotropic diffusion (bottom), a single particle is more likely to move along a certain pathway, aligning with the cellular architecture.

6.1.3 CLARITY

Example questions answered:

“Do neurons in layer 5 of motor cortex send axonal projections into the spinal cord?”

The methods described above only provide rough anatomical information, and therefore have limits to their value. CLARITY is a revolutionary anatomical technique that gives microscopic level analysis. First published in 2013, CLARITY was developed at Stanford by the lab of Dr. Karl Deisseroth. The value behind CLARITY is that we are now able to visualize connectivity in the brain at a microscopic level, giving us amazing spatial resolution at the order of a microns.

One of the problems with visualizing the structures of the brain at a microscopic scale is that cells have a lot of membrane, which is mostly made up of lipids. Instead of letting light pass unimpeded, lipids refract light in somewhat unpredictable ways. Even cytosol has all sorts of particles floating around in it that cause light to bend and bounce around. These lipids and other cellular particles prevent light from passing through nervous tissue, minimizing our ability to use transmitted light to see the brain.

In CLARITY, the brain is first flushed with chemicals that form a gel matrix that surrounds every cellular structural component, from the spines on the dendritic arbor all the way to the axonal terminals. Then, using a chemical detergent, the cellular lipids get solubilized and washed away while the gel matrix remains unaffected. This allows us to now see the “mold” that remains around where the cell membranes used to be. By washing away the light-deflecting lipids, we can now see where the connections were, causing the brain to appear transparent.

Unlike the CT scan, CLARITY can’t be applied in an intact living organism. CLARITY is an extremely destructive process that destroys tissue. The surrounding gel matrix is like a mold of a hand. You can see all the anatomical features of the hands - fingers, wrinkles, nails, and so on. But the mold is just an image, unable to function. The mold of the hand cannot grip things, cannot feel things, and does not have any bones / tendons / muscles. In using CLARITY, all function is destroyed.

Figure 6.12 With CLARITY, a whole animal brain (left) can be made transparent (middle), allowing for visualization of individual cellular structures (right).