Brain Imaging Alphabetical Soup: Making Sense of CAT, PET, MRI, fMRI, SPECT: MRI

I started this mini-series with the articles on how imaging got started, and on CT scans. Now we’ll move on to MRI scans.

MRI, or magnetic resonance imaging, is used to create images of the body’s tissues, specifically of the soft tissues, like organs. X-rays pass through soft tissues undistorted and relatively easily. Now, most human tissue is water-based (which makes sense considering we’re 70% water).  The amount of water in tissues differ. So different tissues will behave differently. These differences can then be used to construct a 3D image.

MRI scans are constructed by applying a strong magnetic field around the body. In water, you can find single protons (Hydrogen atoms, like H20). In MRI scans, it is the H nuclei that create the signal.

So, initially, the fields are randomly oriented. When a strong external magnetic field is applied, a fraction will organize themselves, and align themselves with the external field. This external field is applied in a constant manner throughout the scanning session.

Now, when the protons are aligned, a brief radio frequency is applied. This radio frequency then knocks the protons out of alignment by 90 degrees to their original orientation. So now the protons are spinning in this new state, and as they do this, they produce a detectable change in the magnetic field. This then is what forms the MRI signal.

Eventually, the protons are pulled back into their original alignment (they “relax”). The MRI scanner then repeats the process by sending the radio frequency to excite the protons in different slices of the brain that is being scanned.

Now there are different types of MRI scans, including the T1 and T2 scans.

T1-weighted images are used for structural imaging of the brain. In a T1-weighted image, gray matter looks gray, and white matter looks white. Pretty simple to distinguish.

When the protons are misaligned at 90 degrees to the magnetic field, the MRI signal decays because of interactions with other nearby molecules. This is the T2 image.





Don’t learn to code

With the push to learn code, which I am now a part of, I think we have lost sight of what it means to be a computer programmer.

My SO sent me this link, which I think makes sense: Don’t learn to code. Learn to think.

I think it is well worth a read:


Look at the right side of your body. It’s yours, right? Or maybe it’s your neighbor’s…


Somatoparaphrenia is caused by damage to the right parietal lobe. The similarity of this disorder to BIID, coupled with the childhood onset of these disorders, suggest both may be congenital disorders, that is, present from birth. The disorder is a delusional belief concerning the contralateral lesional side of the body, meaning that the side of the body opposite the side of brain damage is affected.


This disorder should not be confused with asomatognosia, which is unawareness, rather than delusional disbelief, of a limb, usually the left arm.


Patients with somatoparaphrenia deny ownership of either a limb on one side of their body, or an entire side of their body. A sufferer might be adamant that their right arm and leg are not theirs, not part of their many cases, the denial of ownership is of a paralyzed limb. Often, it is the left arm that is denied, as this disorder comes up often in right-brain-damaged patients. The denied limb may even be treated as an individual, given a name, treated as a child and taken care of. This shows how much the patients really dissociate themselves from ownership of the limb.


What do you think some of these sufferers ask for in terms of treatment? You guessed it: amputation. Again, the ethical issues that come up in BIID amputations apply to somatoparaphrenia as well.


One individual, suffering not only from somatoparaphrenia, but also schizophrenia, believed his right arm and foot did not belong to him. He said that his arm belonged to a woman he knew named Maria, and that his foot could not belong to him because it was a “big foot only suited for work.” This case is considered one of the few in which schizophrenia and somatoparaphrenia are documented in the same individual.


You may think, “Well, why don’t you try to ‘prove’ to the patient that their limb is theirs? Why, you can pinch their denied arm, or kick their denied foot. Or you can hold up a mirror to them and ask them to move their denied limb. And once they realize they can move that limb, voila! Problem solved.”


If you thought something along those lines, you were thinking like a researcher. Problem is, even if these things are done to the patient, they still deny ownership of the affected limb.


 However, there has been some success with a mirror experiment. This experiment was the first to describe that viewing a limb through a mirror alters limb disownership of a previously denied limb. What was done was a simple technique:

Take two groups of somatoparaphrenia patients. One group viewed their denied hand as it lay on a table. The second group also laid their denied hand on a table, but in front of them was a mirror which reflected their hand. The patient then viewed their affected limb in the mirror. There was no way for the mirror-group patient to look at their hand because a cardboard cutoff was placed around their neck to prevent them from being able to see below their neck. The results are startling: the first group, with no mirror, continued to deny their limb. But the mirror group accepted their limb as their own, so long as they viewed it through the mirror. If they stopped viewing their limb in the mirror and looked down at their hand on the table, they reverted back to denying their hand.


This mirror experiment is very interesting and is reminiscent in some ways of the rubber hand technique. This technique goes something like this:


Stick someone in a chair in front of a table. On the table is his left hand, hidden from his view by a screen. On the table is a lifelike rubber left hand and arm. The subject focuses their eyes and attention on the rubber hand and arm. A scientist stroke both the person’s hand and the rubber hand simultaneously, in the same area of the hand. Guess what happens?


The person feels a sense of ownership of the rubber hand. As one subject put it: “I found myself looking at the dummy hand thinking it was actually my own.”


The rubber hand illusion suggests that our self-awareness of our body can be manipulated and even altered through the senses. In effect, the brain uses the sensory modalities to construct and distinguish self from non-self. What do you think this mean in terms of somatoparaphrenia?

Ancient Egypt and Neuroscience

When you think of Ancient Egypt, you probably conjure up images of hieroglyphics, the Sphinx, pyramids. Maybe you’ll imagine an embalmer burning the midnight oil, hunched over a corpse, candles flickering all around, casting shadows.

And if you think of the brain in relation to the Egyptians, you’ll most likely imagine a hook going up a body’s nose, pulling out the brain bit by bit.


But the Ancient Egyptians knew more about the brain than how to pull it out with a hook up the nose.


The Ancient Egyptian Book of the Dead was not written as one whole book. Instead, the book is made up of scrolls of papyrus that have been found buried with the dead. The Book is a collection of spells and incantations, meant to be recited by the departed, to ease them through their journey into the afterlife.

But what is more interesting is that the Book of the Dead may have described spinal surgery, reflected in one of the scrolls about Osiris, the god related to the cycle of harvest, regrowth and rebirth, an apt role for the god presiding in the afterlife and the world of the dead.


The assembly of Osiris’ spine was described in the Book. Osiris, husband and brother to Isis, the mother god of Egypt, is also brother to Seth. Seth becomes jealous of the relationship between Osiris and Isis and decides to kill him. At a feast, Seth persuades Osiris to lie down in a sarcophagus. When he does, Seth quickly closes the lid over the sarcophagus, thereby killing Osiris. The sarcophagus is sent out to sea, where it washes up in Byblos (in modern-day Lebanon). Osiris and his sarcophagus become part of a tree in the royal palace.


Isis mourns the loss of Osiris and searches the world for his remains. When she finds him in the royal palace of Byblos, she reclaims his remains and his sarcophagus, taking them back to Egypt.


But Seth finds out and cuts Osiris’ body into thirteen parts, scattering them all over Egypt. Determined, Isis scouts the land for the body parts, finding twelve of them. The thirteenth, the spine, is never reclaimed since it was eaten by a crocodile.

With Thoth, the god of medicine, Isis recreates Osiris’ spine and resurrects him. But the problems are not over.


Osiris resides in the underworld, determining each dead person’s fate based on their righteous and unrighteous deeds. Through immaculate conception, Isis finds herself with child and gives birth to a baby boy named Horus. To escape Seth’s wrath, Isis hides baby Horus in a basket in the reeds of the Nile River. Horus survives and eventually fights Seth. During battle, Seth gouges out one of Horus’ eyes. Ever faithful Thoth, though, is able to restore Horus’ eye. (Incidentally, the restoration of Horus’ eye has become the symbol of modern-day prescriptions, the Rx.)


What is interesting is that Osiris’ resurrection is symbolized by the djed column, which is a cross with four bars perpendicular to a tall one. The djed column is symbolic of the spine and the ribs of Osiris, and was painted on sarcophagi to express desires for the dead to be resurrected, that is, live for eternity, in the underworld, just like Osiris.


The Egyptians knew about the relationship between spinal injury and paralysis. They also knew that sprains and wounds of the spine could be treated, and they had recommendations on treatment options. But they knew that paralysis due to spinal injury was not treatable. This is not so different an analysis to the modern-day, though now we have some options arising in the field of neuroengineering. Today, there are some treatment options emerging that uses neuroprosthetics to allow an injured person to command a robotic limb with just thought, just as you and I are able to move by just thinking about movement.


I cannot talk about the ancient Egyptians and their contributions to medical science without referencing the Edwin Smith Papyrus. This medical treatise not only contains the first written use of the word “brain,” but it is also a collection of forty-eight patient cases with head, spinal, neck, and other injuries. One case describes how a patient can be left without speech after a wound suffered to the temple. This is consistent with today’s findings that the language centers of the brain are found in the temporal lobe (usually the left temporal lobe).


The Edwin Smith Papyrus had three diagnostic conclusions:

That the patient be told a particular injury is


“an ailment that I will treat”

“an ailment that I will not try to treat,”


“an ailment that I will not treat.”


In case six, where the word “brain” is first used, a male patient has had a wound to his head, “penetrating to the bone, smashing his skull, (and) rending open the brain of his skull.”


The examination describes this:


“If thou examinest a man having a gaping wound in his head, penetrating

to the bone, smashing his skull, (and) rending open the brain of his skull, thou shouldst

palpate his wound. Shouldst thou find that smash which is in his skull [like] those

corrugations which form in molten copper, (and) something therein throbbing (and)

fluttering under thy fingers, like the weak place of an infant’s crown before it becomes

whole-when it has happened there is no throbbing (and) fluttering under thy fingers

until the brain of his (the patient’s) skull is rent open-(and) he discharges blood from

both his nostrils, (and) he suffers with stiffness in his neck…”


The diagnosis: Tell him that his wound is “an ailment not to be treated.”

But the wound could be anointed with grease, and no bindings should be put on it.


Case 29 describes “a gaping wound in the vertebra” of a patient’s neck.


The examination describes this:


“If thou examinest a man having a gaping wound in a vertebra of his

neck, penetrating to the bone, (and) perforating a vertebra of his neck; if thou examinest

that wound, (and) he shudders exceedingly, (and) he is unable to look at his two

shoulders and his breast…”


The diagnosis: Tell the patient that his wound is “an ailment with which I will contend.”

The treatment includes binding the wound “with fresh meat the first day.”

Another case, case forty-eight, describes a sprain in the vertebra of the spinal column:


“If thou examinest [a man having] a sprain in a vertebra of his spinal

column, thou shouldst say to him: “Extend now thy two legs (and) contract them both

(again).” When he extends them both he contracts them both immediately because of

the pain he causes in the vertebra of his spinal column in which he suffers.”



The diagnosis: Tell the patient that his injury is “an ailment which I will treat.”

The treatment includes placing the patient prostrate on his back.



The Edwin Smith Papyrus holds information about head trauma cases and neck injuries



The Edwin Smith Papyrus is not the only ancient Egyptian written work that has references to the spinal cord.


Even with the emphasis on head injuries described in the Edwin Smith Papyrus, the ancient Egyptians still believed that it was the heart, not the brain, that was the seat of intellect and sensation. This is evidenced by the famous Egyptian practice: mummification. The first step was to remove the brain through the nose using a long hook. In contrast, the heart, as well as other organs, was wrapped and placed in canopic jars for the dead to use in the afterlife. The brain was disposed of.


This view that it was the heart that was the mind was held even by the great Greek philosopher Aristotle, who maintained that the brain was only a cooling radiator for the body. This view of the heart versus the brain persisted for over one thousand years and traversed not just the Egyptian and Greek cultures.


Brain Imaging Alphabetical Soup: Making Sense of CAT, PET, MRI, fMRI, SPECT: CAT Scans

We’ve all heard the abbreviations: CAT, PET, MRI, fMRI, SPECT.

Now what the heck do they all mean?

Brain imaging has an interesting start. But generally, brain imaging techniques fall into two broad categories: Structural imaging, and Functional imaging. Structural imaging does just what its name implies: it provides images of the structure of the brain. There’s no indication of blood flow or brain metabolism here; just bone and tissue. Structural images are based on the idea that different bodily tissues have different densities and different physical properties. Structural images provide static, one-shot images of the brain’s structure. They say nothing of function.

Functional imaging also does what its name implies: it images the brain as it functions. Dyes, radioactive tracers, are all used in these imaging modalities to image the brain’s blood flow and metabolism. These images are dynamic, showing changes in brain function over a period of time.

The next few articles in my blog will feature one of the imaging techniques in an article. We’ll start off with CAT scans.

CAT stands for Computerized Axial Tomography. CAT scans are also abbreviated CT scans, for Computerized Tomography. CT scans are possible because different tissues have different X-ray absorptions. How much a tissue absorbs X-rays is related to that tissue’s density. So, bone absorbs the most X-rays, cerebrospinal fluid (CSF) absorbs the least. That’s why on CT scans, bone appears white and the ventricles, which contain CSF, appear black.

There’s a slight danger with CT scans, because the person being imaged is exposed to a slight amount of radiation.


CT scan image can be found here:

Mosso and Bertino: Brain Injury to Imaging Inventions

The earliest ways of peering into the brains of people was invasive, and sometimes, fatal. Consequently, most subjects were those who were mentally disabled, those who had mental illnesses. Therefore, we now know more about dysfunction than we do function. However, this isn’t a bad thing, considering that it’s through dysfunction that we can better understand how a healthy brain works.


There was an 18oo’s experimenter, Angelo Mosso. Mosso had the chance of encountering a peasant named Bertino. Now, Bertino suffered a head injury several years prior to meeting Mosso. The injury was severe enough that it destroyed his frontal bone of his skull, which cover the frontal lobe. The frontal lobe is for reasoning, decision-making, planning, all the executive functions, and personality. What was most interesting to Mosso, however, was the fact that because Bertino had this bone injury, his frontal lobes were now covered not by bone, but by fibrous tissue. This tissue acted as a window through which Mosso could see Bertino’s brain pulsating.

I’m sure if you saw a pulsating brain, you’d investigate further. And that’s exactly what Mosso did.

So one day, Mosso noticed that tere were changing in the pulsation magnitude: whenever the church bells rung at noon, the pulsating increased. So what does Mosso do?

He asks Bertino a question: does the ringing of the church bells remind you of your obligation to silently recite the Ave Maria?

To which Bertino responds: Yes.

And as Bertino responded, the pulsations increased once more.

So of course Mosso is ultra-curious now. He asks Bertino some math questions, like multiply this by that. Whenever Mosso asked a question, the pulsations increased. Whenever Bertino answered a question, there was another pulse magnitude increase.


If you made these observations, what would you hypothesize was going on?


This was Mosso’ hypothesis, which proved to be correct: an increase in blood flow to the brain could provide a measure, albeit indirect, of brain function during a specific activity.


Mosso was right and people began developing techniques for measuring blood flow to the brain. This led to our current technologies, such as PET, fMRI, and SPECT.

 Image is from Wikipedia, Angelo Mosso article.





A neuron can be represented as an electrical equivalent circuit

A neuron can be represented as an electrical equivalent circuit, which is a mathematical model that represents all of the major electrical properties of a given neuron. An equivalent circuit is made up of batteries, capacitors and resistors.

Basically, the model gives us a relatively intuitive idea of how currents are caused by ionic movement and how that generated nerve cell signaling. The model also gives us a quantitative way of modeling current and ionic movement, in relation to neuronal functioning.

To develop an equivalent circuit, you have to relate a membrane’s physical properties to its electrical properties. So, consider the lipid bilayer. It gives a membrane capacitance, which is the ability to store charge. Another way of understanding capacitance is that it is the ability of an insulator to separate electrical charge on either side of it.

So, the nonconducting bilayer separates the cytoplasm and the extracellular fluid. Both fluids are conductive, so the presence of a layer that separates them acts as a capacitors, which then gives rise to the electrical potential difference across the membrane.

The membrane, though, is a leaky capacitor, because it has ion channels, which endow the membrane with conductance and the ability to generate electromotive force.

(a source of electrical potential is called an electromotive force, and an electromotive force generated by a chemical potential difference is called a battery)