Sunday, January 22, 2012

Brain : CT MRI

Authors : Drs Christopher P. Hess and Derk D. Purcell University of California SF


Brain : CT MRI

Noninvasive imaging of the central nervous system

The structure and function of the brain can be studied noninvasively by doctors and researchers using computed tomography (CT) and magnetic resonance imaging (MRI). This Knol discusses how images of the brain are generated using these techniques, provides examples of the different types of information that can be revealed, addresses the relative strengths and weaknesses of each modality for evaluating several common disorders of the central nervous system, and covers some of their potential risks. A high-resolution atlas of MRI anatomy is also included.


The complexity of the organ that determines how a person thinks, moves, feels and remembers is overshadowed only by its unique vulnerability. The brain is hidden from direct view by the protective bony covering of the skull, which not only shields it from injury but also hinders the study of its function in both health and disease. The cells in the arteries that supply the brain are so tightly bound that even most normal cells in the bloodstream are prevented from crossing the so-called “blood-brain barrier,” thereby rendering the normal chemistry of the brain invisible to the routine laboratory blood tests that are often used to evaluate the heart, liver or kidneys.

Computed tomography (CT) and magnetic resonance imaging (MRI) have revolutionized the study of the brain by allowing doctors and researchers to look at the brain noninvasively. Like other organs in the human body, the structure of the brain is highly organized according to its function. Different parts of the brain play specific roles that govern different activities, such as movement, cognition, and vision. These imaging techniques have allowed for the first time the noninvasive evaluation of brain structure, allowing doctors to infer causes of abnormal function due to different diseases.

How are brain images made with CT?

ABOVE: A patient undergoing CT examination of the head. The patient's head is positioned centrally within the gantry of the CT scanner as he lies on his back, and the table moves horizontally as the images are rapidly obtained. With modern CT methods, the entire examination may take less than 15 seconds. (Click on image for a movie of the scan.)

Computed tomography is based on the measurement of the amount of energy that the head absorbs as a beam of radiation passes through it from a source to a detector. Within a CT scanner, the radiation source and detector are mounted opposite one another along a circular track, or
gantry, allowing them to rotate rapidly and synchronously around the table on which the patient lies. As the x-ray source and detector move around the patient’s head, measurements consisting of many projections through the head are obtained at prescribed angles and stored on a computer. The table moves horizontally in and out of the scanner in order to cover the entire head [1, 2].

The “tome” in tomography is the Greek word for “slice.” At the core of the scanner is a computer that not only controls the radiation source, the rotation of the x-ray tube and detector, and the movement of the table, but also generates anatomical slices, or
tomograms, from the measured projections. The mathematical technique that allows an image of the head to be recovered from its projections is referred to as the backprojection algorithm [3]. Because the patient is positioned horizontally on the table, the backprojection algorithm yields slices that are transaxial, which means the slices are oriented at right angles to the long axis of the body.

The primary physical quantity that is captured with CT is density, or mass per unit volume. Prior to display and storage of CT images, pixel intensities are mapped to a standard numerical scale to allow reliable discrimination between different densities of tissue such as air, water, fat, bone, and various brain constituents. When the images are reviewed on a computer, the intensities are further modified by a process referred to as windowing in order to optimally depict the density of different tissues for visual display. Extremely dense material, such as metal or bone, appears bright on CT images, whereas tissue that is less dense, like fat or water, appears dark.
ABOVE RIGHT: A single slice from a normal head CT at brain window (left) and bone window (right) settings. Arrows indicate tissues of different density, including water, fat, soft tissue and bone.

How are brain images made with MRI?

ABOVE: A patient undergoing an MRI examination of the head. The patient's head is positioned in the center of the scanner tube as he lies on his back. The noise heard during the exam comes from the electronic switching of magnetic coils inside of the tube, and not from moving parts. Earplugs should be worn to prevent hearing damage. (Click on image for a movie of the scan.) 
Magnetic resonance imaging relies upon signals derived from water molecules, which comprise between 70% and 80% of the average human brain. This ubiquitous biological molecule has two protons, which by virtue of their positive charge act as small magnets on a subatomic scale. Positioned within the large magnetic field of an MR scanner, typically 30 to 60 thousand times stronger than the magnetic field of the earth, these microscopic magnets collectively produce a tiny net magnetization that can be measured outside of the body and used to generate very high-resolution images that reveal information about water molecules in the brain and their local environment.

Protons placed in a magnetic field have the interesting property that they will absorb energy at specific frequencies, and then re-emit the energy at the same frequency. To measure the net magnetization, a coil placed around the head is used to both to generate electromagnetic waves and measure the electromagnetic waves that are emitted from the head in response. Unlike CT, which uses x-rays with very high frequency energy, MRI uses electromagnetic waves in the same portion of the electromagnetic spectrum as broadcast FM radio.

MRI is also a tomographic imaging modality, in that it produces two-dimensional images that consist of individual slices of the brain. Images in MRI need not be acquired transaxially, and the table or scanner does not move to cover different slices in the brain. Rather, images can be obtained in any plane through the head by electronically “steering” the plane of the scan. Precise spatial localization is achieved through a process termed
gradient encoding [4]. The switching on and off of these magnetic field gradients are the source of the loud clicking and whirring noises that are heard during an MRI scan. While this process requires more time than CT scanning, imaging can be performed relatively rapidly using modern gradient systems [5].
Image intensity in MRI depends upon several parameters. These are proton density, which is determined by the relative concentration of water molecules, and T1, T2, and T2* relaxation, which reflect different features of the local environment of individual protons. The degree to which these parameters contribute to overall image intensity is controlled by the application and timing of radiofrequency energy through different pulse sequences. The most commonly used pulse sequences in brain imaging preferentially emphasize T1 relaxation, T2 relaxation, T2* relaxation or proton density. Specialized pulse sequences can sensitize images to flowing blood, minute changes in local brain oxygen content, or even to the microscopic movement of water molecules within the brain. Each pulse sequence confers a different contrast weighting to the image, such that when combined, the aggregate intensities from the different pulse sequences allow inference about the properties and local environment of the brain tissue being studied. For example, using MRI, one can infer the phase (solid or liquid), content (fat, water, air, blood) or movement (static or pulsatile) of a given structure in the brain.  
ABOVE RIGHT: Selected images from a brain MRI obtained in a normal volunteer, all acquired at the same level through the head. Proton density (PD, top left), T1-weighted (T1, bottom left), T2-weighted (T2, top right), and MR angiography (MRA, bottom right) scans have very different image contrast that reveals specific information about various structures in the brain.

What is a contrast agent?

Contrast media, or “dyes” are used both in brain CT and MRI to provide another mechanism for modulating image intensity beyond what is possible using intrinsic tissue contrast. These are externally administered pharmaceutical agents given during an imaging examination to highlight normal or diseased brain structures. The additional information provided by a contrast agent may or may not be necessary to make an accurate diagnosis.
Contrast agents are most often administered by intravenous injection, but may in certain cases require intrathecal (spinal) injection using a lumbar puncture (spinal tap) procedure. Because they are water soluble they are normally removed from the body by the kidneys, though when the kidneys are diseased the liver may also contribute to their elimination. CT contrast agents are typically iodine-containing compounds that transiently increase the density of structures that they pass through. MRI contrast agents contain the heavy metal gadolinium, which changes the inherent T1 and T2 relaxation parameters of tissues.

The normal path of intravenously-injected contrast agents is through the heart, lungs and arteries of the chest and neck before entering the head. Once in the head, contrast passes first into the arterial system of the brain and its coverings, then through the cerebral microcirculation to supply the brain itself, ultimately passing into the intracranial venous system. Once it has passed into the large veins in the head, contrast is transmitted into the veins of the neck. From there, the contrast enters the heart for the second time, beginning the process of
recirculation. The relative timing of the scan with respect to the location of the contrast agent within the blood pool allows detailed imaging of the arteries, brain, or veins.
ABOVE : Unenhanced (labeled “-”) and contrast-enhanced (labeled “+”) images from CT (top row) and MRI (bottom row) in two different patients with brain tumors. Contrast enhanced images show both normal blood vessels (red arrows) and tumor enhancement from breakdown of the blood-brain barrier (yellow arrows).

Contrast agents in neuroimaging are usually given to evaluate blood vessels or to assess the integrity of the blood-brain barrier. In the former case, CT or MR angiography can diagnose cerebral aneurysms, vascular malformations, and narrowed or occluded arteries. In the latter, enhancement of the brain itself is used for the diagnosis of disease. The cells that line the capillaries of the normal brain are tightly bound together to form the “blood-brain barrier,” which allows the passage of oxygen and nutrients into the brain but prevents the transit of disease-causing organisms and large molecules, including contrast agents. Brain tumors, infections and inflammatory processes often disrupt the blood-brain barrier, giving rise to abnormal enhancement within the brain.

What do brain CT and MRI images show?

Interpretation of brain images requires a detailed knowledge of anatomy and a comprehensive understanding of how different diseases affect the brain and its supporting structures. Radiologists are medical doctors who specialize in acquiring and interpreting images; neuroradiologists focus specifically on imaging of the nervous system. These specialists work together with neurologists, neurosurgeons and primary care physicians to use CT and MRI to diagnose disorders of the brain and understand their significance for patients. Several different anatomical structures are routinely visualized with neuroimaging:

THE BRAIN. The gray matter of the brain consists of the cortex that lines the external surface of the brain and the gray nuclei deep inside of the brain, including the thalami and basal ganglia. Within the gray matter lie the cell bodies of the roughly 85 billion neurons that constitute the processing engine for the brain. White matter is comprised of the neuronal axons that interconnect different regions of the brain and serve as the interface between the brain and the rest of the body. Different diseases affect the gray and white matter in distinct patterns. RIGHT: MRI in a patient with a brain tumor (*) that crosses the midline of the brain to involve both hemispheres. (Click on image to enlarge.)
BLOOD VESSELS. The arterial supply to the brain arises from paired carotid and vertebral arteries in the neck. These four vessels continue into the head and divide into separate anterior, middle and posterior cerebral arteries that provide oxygen and nutrients to different regions of the brain. These vessels are interconnected at the base of the brain through a network of arteries called the circle of Willis. The principal veins within the head, the dural venous sinuses, collect blood that has passed through the brain. Blood vessels may cause symptoms by becoming enlarged or narrowed, occluded, or by supplying vascular malformations in or around the brain. RIGHT: MRA scan from a patient with a large tangle of abnormal blood vessels inside of the brain (*) called an arteriovenous malformation. (Click on image to enlarge.)
BRAIN COVERINGS. The brain is not rigidly adherent to the skull. It is surrounded by three layers of covering: the innermost pia mater, the middle arachnoid mater, and the outermost dura mater. Cerebrospinal fluid (CSF), a translucent liquid derived from blood and contained within the space between the pia and arachnoid mater, serves as a chemical and physical cushion for the brain. Blood from ruptured aneurysms, trauma or pus from infections such as meningitis may collect within the spaces between meningeal layers or within the CSF. RIGHT: Slice from a CT in a patient who experienced a sudden severe headache from a ruptured aneurysm. There is high-density blood outside of the brain and blood vessels (yellow arrow) where there is normally low-density CSF (red arrows). (Click on image to enlarge.)
THE SKULL. The bones that surround the brain, including the calvarium, facial skeleton and skull base, are collectively referred to as the skull. These structures provide protection for the brain and a rigid frame to support the functions of the face. Because cortical bones contain very little water, they are evaluated reliably only with CT. The marrow within these bones, however, can be seen on MRI images. Bones can be the primary source of disease, or they can be secondarily involved by different infections and tumors, for example. RIGHT: The image on the left shows a slice from a CT in a patient with kidney cancer. The yellow arrows point to a tumor in the right skull bone from a metastasis. (Click on image to enlarge.)
SURROUNDING TISSUES. The skull is surrounded not only by the scalp, but also fat, muscles, blood vessels, and various special glands. Importantly, the front of the head contains an array of muscles, salivary glands, and lymph nodes that may be primarily or secondarily affected by various disorders. The physical location of abnormalities in these regions often gives clues as to the source of disease. RIGHT: Slice from a contrast-enhanced MRI in a patient with severe left eye swelling and pain from an infection. Within the red circled area, there is abnormal enhancement of the fat that surrounds the eyeball. The yellow arrow points to normal fat behind the right eye. (Click on image to enlarge.)

Examples of head CT and MRI

Head CT example
Click on the images below for movies of normal noncontrast, postcontrast, and CT angiogram examinations of the brain. Note that CT angiography provides very high-resolution images of the arteries and veins of the brain. By convention, axial images are displayed such that the left side of the brain is on the right side of the image. This is equivalent to looking up through the feet, abdomen, chest, and neck directly into the slice. (From left to right: head CT without contrast, head CT with contrast, and head CT angiogram images.)

Head MRI example
Click on the images below for movies of normal proton density, T1-weighted, T2-weighted, T2 FLAIR, and MR angiography examinations of the brain. Note that FLAIR is a technique that causes the CSF to be dark, making it easier to identify abnormally bright areas of the brain. MR angiography of the brain is different from CT angiography because it usually does not require contrast, but rather sensitizes the scan to normal flowing blood. (Clockwise from left: sagittal T1, axial proton density, coronal T2, axial MRA, and coronal FLAIR MRI images).

High-resolution Atlas of MRI Anatomy 
Clink on the images below for high-resolution movies of MR images through the brain in the axial, coronal, and sagittal imaging planes. Note that coronal images appear as if one were looking at the patient face on, with the left side of the patient’s head on the right side of the image and the right side of the patient’s head on the left side of the image. Similarly, sagittal images are displayed as if one were looking at the patient from the side. The anatomy is labeled in detail to indicate some of the most common areas of the brain that are involved by different diseases.

Is CT or MRI better for imaging the brain?

The answer to this question depends on the purpose of the examination. CT and MRI are complementary techniques, each with its own strengths and weaknesses. The choice of which examination is appropriate depends upon how quickly it is necessary to obtain the scan, what part of the head is being examined, and the age of the patient, among other considerations. All imaging studies that are not performed for research should be obtained in close consultation with a physician. Both techniques are designed to examine specific problems. The utility of “screening” CT or MRI, in which a scan is obtained in a healthy patient without any symptoms to look for a brain tumor or any other condition, has not been established.

The advantages of each modality listed below serve as general guidelines that doctors use to decide between head CT and MRI:

Advantages of head CT
  • CT is much faster than MRI, making it the study of choice in cases of trauma and other acute neurological emergencies
  • CT can be obtained at considerably less cost than MRI, and is sufficient to exclude many neurological disorders
  • CT is less sensitive to patient motion during the examination. because the imaging can be performed much more rapidly
  • CT may be easier to perform in claustrophobic or very heavy patients
  • CT provides detailed evaluation of cortical bone
  • CT allows accurate detection of calcification and metal foreign bodies
  • CT can be performed at no risk to the patient with implantable medical devices, such as cardiac pacemakers, ferromagnetic vascular clips, and nerve stimulators

Advantages of head MRI
  • MRI does not use ionizing radiation, and is thus preferred over CT in children and patients requiring multiple imaging examinations
  • MRI has a much greater range of available soft tissue contrast, depicts anatomy in greater detail, and is more sensitive and specific for abnormalities within the brain itself
  • MRI scanning can be performed in any imaging plane without having to physically move the patient
  • MRI contrast agents have a considerably smaller risk of causing potentially lethal allergic reaction
  • MRI allows the evaluation of structures that may be obscured by artifacts from bone in CT images

Specific situations in which CT or MRI may be preferred
  • Acute hemorrhage. While it is widely held that CT is more reliable than MRI in the detection of acute bleeding, recent studies have shown that MRI is at least as sensitive as CT [6]. Nonetheless, CT is generally preferred as it can more rapidly identify patients that require emergency treatment. Examples of brain hemorrhage. RIGHT: The left image (CT) shows a blood clot inside of the brain due to high blood pressure (*) with different densities of layering blood (yellow arrows). The right image (FLAIR MRI) shows blood outside of the brain caused by a ruptured aneurysm (arrows).
  • Traumatic brain injury. CT is also preferred to MRI in cases of acute head injury, when it is necessary to rapidly triage patients requiring emergency surgery [7]. In the weeks to months following head trauma, however, MRI is a more sensitive tool to evaluate for the presence of chronic hemorrhage and subacute shear injury. Examples of traumatic brain injury. RIGHT: The image on the left is a CT that shows a large subdural hematoma (*), a collection of blood between the brain and skull, as well as subarachnoid blood (yellow arrows) in a patient who fell from a second-story window. The MRI on the right illustrates tiny areas of “shear” injury (arrow) in a patient who was in a car accident two months prior.
  • Stroke. The initial treatment of acute stroke, or “brain attack,” hinges upon distinguishing whether the symptoms are due to a blood clot in a vessel or another cause such as hemorrhage. By virtue of its speed and accuracy, CT continues to be the mainstay of diagnosis in this disease. Newer approaches such as CT angiography and CT perfusion further augment the role of CT in the early diagnosis of stroke [8]. In head-to-head trials, however, diffusion-weighted MRI has been shown to be more sensitive for identifying early stroke [9], but is used in very few centers because it can not be obtained as rapidly as CT. RIGHT: Examples of stroke on CT and MRI. On the left, low density in the brain (*) was caused by a stroke two days prior. On the right, diffusion-weighted MRI shows a large stroke (*) in a patient who was abruptly unable to move her right arm or speak one hour prior to the MRI.
  • Seizures. The imaging evaluation of seizures depends upon the age of the patient and the chronicity of symptoms [10]. Most first-time seizures are caused by fever in the pediatric population, and by metabolic abnormalities or medications in the adult population. CT is useful in this case to exclude rare secondary causes for acute seizures such as brain tumor, brain infection, or stroke. When seizures are longstanding, MRI is more sensitive in the assessment for structural sources for seizures. RIGHT: Two patients with seizures. CT obtained in the first patient (left) shows several metastases (arrows) as the cause for first-time seizure. The MRI image on the right, obtained in a patient with chronic seizures, shows a subtle abnormality (red arrow) in the hippocampus.
  • Brain tumors. MRI is the modality of choice in the evaluation of known primary brain tumors and metastases, as it allows more accurate delineation of tumor margins and provides more information with which to differentiate between various tumor types [11]. RIGHT: CT and MRI images from the same patient show subtle low density (circle) in the brain on CT, but a more extensive abnormality on MRI (*) corresponding more accurately to the true extent of disease.
  • Infection. Brain infection can be caused by bacteria, viruses, parasites, and other microbes. CT may be used to determine complications related to infections, but is not as sensitive as MRI in the initial detection of infection [12]. Certain types of infection have a characteristic appearance on MRI, such as brain abscess or encephalitis. RIGHT: Two patients with altered mental status and fever. CT (left) shows an abscess in the left frontal lobe (arrows) causing the brain to shift to the right side. MRI (right) illustrates an extensive signal abnormality in a typical distribution for herpes encephalitis.
  • Immunocompromised patients. Dysfunction of the immune system (which can be caused, for instance, by blood cancers, chemotherapy, organ transplant, or HIV) predisposes patients to infections that a healthy immune system is normally able to fight off. In addition, some cancers are more common among the immunocompromised. It may be difficult in some situations to distinguish between these two entities on both CT and MRI. CT is most useful in the acute setting, but MRI again has higher sensitivity. RIGHT: CT (left) and MRI (right) obtained in two different HIV+ patients. Ring-like calcification (arrow) and more subtle enhancement (circle) in the first patient are due to recurrent infection (toxoplasmosis). More solid regions of enhancement in the second patient are due to brain cancer (lymphoma).
  • Pediatric patients. Because pediatric patients are particularly sensitive to the effects of radiation, MRI is the preferred modality for the evaluation of the brain in children. In general, neurological disorders in children are very different from those in adults. For example, children are more likely to have different types of brain tumors than adults, and certain congenital abnormalities of the brain are typically detected in childhood. RIGHT: Image on the left shows a CT obtained in a one year old with a brain tumor causing distention of the ventricles (*) and marked thinning of the normal brain (arrows). On the right, an MRI obtained in a fetus inside of the mother's uterus shows a structural brain abnormality called callosal agenesis.

What are the risks of brain CT and MRI?

  • CT requires the use of ionizing radiation, which has a very low risk of damaging the brain and other incidentally exposed body tissues by causing damage to DNA. The growing use of CT in medicine and the development of newer techniques that require higher radiation exposure have recently increased awareness of the risks of CT [13].
  • The dose of radiation to a patient during head CT depends upon the type of scan obtained and the machine settings, but average approximately 180 millirems. (A millirem is a very small unit used to quantify the effect of radiation on the human body.) For comparison, the annual individual effective dose due to natural background radiation is approximately 360 millirems.
  • The exact risk of the small radiation exposure due to head CT is difficult to calculate. In the highest estimates, a single head CT has been associated with a roughly 0.07% lifetime risk of cancer in a one-year old child, though the exact number is controversial [14]. For comparison, the lifetime risk of dying in a motor vehicle accident by a person in the United States is 17 times greater at approximately 1.2% (National Safety Council, 2004 data).
  • Like any pharmaceutical, contrast agents carry a small risk of causing an allergic reaction. Modern x-ray contrast agents cause allergic reactions in between 4% and 8% of patients, typically causing minor rashes or itching. More serious allergies, such as difficulty breathing or low blood pressure occur in up to 1% of patients, but death is exceedingly rare (0.001% to 0.009% of patients). Allergic reactions are extremely rare with MRI contrast, occurring in only 0.07% of patients. In patients with kidney disease, CT contrast agents carry the additional potential risk of causing acute renal failure [15] and MR contrast agents may cause a rare disease called nephrogenic fibrosing dermatopathy [16].
  • Because the MRI scanner acts as a powerful magnet, it has the potential to physically move objects that contain iron. To avoid the risk of internal injury, patients are carefully screened for pacemakers and cardiac defibrillators, metal fragments in the eye from sheet metal working, and other types of internal metal prior to undergoing an MRI scan. Similarly, there is a risk of external injury to the body when metal outside of the magnet is brought close to the scanner. Scanners are located in secure rooms and carefully labeled to avoid inadvertent introduction of metals into the magnetic field.
  • Excluding injuries reported from implanted or unsecured ferromagnetic materials, there have been no reports of longstanding detrimental health effects from the high magnetic fields, magnetic gradients, or radiofrequency energy that are used in MRI.
  • Because MRI requires that the patient lie still inside of a narrow tube, claustrophobic patients often find it challenging to complete an entire scan. In these patients and in young children, it may be necessary to administer sedative medication, which also carries risks.
  • In most cases, the benefits of identifying a neurological disease with imaging far outweigh the risks. Nevertheless, it is important to ensure that (1) every scan is absolutely medically necessary and (2) the minimum possible x-ray dose is used for CT, especially in children [17]

More information

Web resources
Books about neuroimaging
  1. Scott W. Atlas. MRI of the Brain and Spine. 3rd ed. Lippincott Williams & Wilkins 2001.
  2. A. James Barkovich. Pediatric Neuroimaging. 4th ed. Lippincott Williams & Wilkins 2005.
  3. Henri M. Duvernoy. The Human Brain: Surface, Three-Dimensional Sectional Anatomy with MRI, and Blood Supply. 2nd ed. Springer, 1999.
  4. Alisa D. Gean. Imaging of head trauma. Lippincott Williams & Wilkins 1994.
  5. Anne G. Osborn. Diagnostic Neuroradiology. 1st ed. Mosby. 1994.
  6. David D. Stark and William G. Bradley, Jr. Magnetic Resonance Imaging. 3rd ed. Mosby 1999.


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