MRI Basics
The way magnetic resonance imaging (MRI) is generated is complicated and is much harder to understand than plain radiography, CT and ultrasound. It has strong underpinnings in physics which must be understood before any real sense of "how it works" is gained. What follows is a very abbreviated or "broad strokes" description of the process. For a more detailed information, please go to our Plane Mathematics, Cross-Sections, and Physics of MRI pages.

A magnetic resonance system (the actual machine) consists of the following components:
 1) A large magnet to generate the magnetic field. 2) Shim coils to make the magnetic field as homogeneous as possible. 3) A radiofrequency (RF) coil to transmit a radio signal into the body part being imaged. 4) A receiver coil to detect the returning radio signals. 5) Gradient coils to provide spatial localization of the signals. 6) A computer to reconstruct the radio signals into the final image.

The signal intensity on the MRI is determined by four basic parameters:
 1) Proton density 2) T1 relaxation time 3) T2 relaxation time 4) Flow

The MRI Simplified

MRI uses a powerful magnetic field that makes the hydrogen protons in water molecules, which comprise between 70% and 80% of the average human brain, line up. This ubiquitous biological molecule has two protons, which by virtue of their positive charge act as small magnets on a subatomic scale. Then once they are all lined up from the magnetic field, they are then knocked out of line by radio waves. When the radio waves are stopped, the protons relax back into line, releasing resonance signals that are transmitted to a computer.

To have a better understanding or image of this, think of the hydrogen proton as if it were a gyroscope or even the planet earth, spinning on its axis, with a north-south pole. In this respect it behaves like a small bar magnet. Now under normal conditions, these hydrogen proton "bar magnets" spin in the body with their axes randomly aligned since nothing is pulling them magnetically in the same direction. An example could be a group of children on a playground running around with no sense of order.

When the body is placed in a strong magnetic field, such as an MRI scanner, the protons' axes all line up. This uniform alignment creates a magnetic vector oriented along the axis of the MRI scanner. Now think of those same children with no order and how each one will line up if someone yells "cookie." How loud you yell "cookie" depends on your strength and this is the same with different machines. Each scanners come in different field strengths, usually between 0.5 and 1.5 tesla (T).

The strength of the magnetic field can be altered electronically from head to toe using a series of gradient electric coils, and, by altering the local magnetic field by these small increments, different slices of the body will resonate as different frequencies are applied.

When additional energy, in the form of a radio wave, is added to the magnetic field, the magnetic vector is deflected. The radio frequency (RF) wave that causes the hydrogen nuclei to resonate is dependent on the element sought (hydrogen) and the strength of the magnetic field.

When the RF source is switched off the magnetic vector returns to its resting state, and this causes a signal, or radio wave to be emitted. It's this signal which is used to create the MR images. Receiver coils are used around the body part in question to act as aerials to improve the detection of the emitted signal. The intensity of the received signal is then plotted on a grey scale and cross sectional images are built up.

Multiple transmitted RF pulses can be used in sequence to emphasise particular tissues or abnormalities. A different emphasis occurs because different tissues relax at different rates when the transmitted RF pulse is switched off. The time taken for the protons to fully relax is measured in two ways. The first is the time taken for the magnetic vector to return to its resting state and the second is the time needed for the axial spin to return to its resting state. The first is called T1 relaxation, the second is called T2 relaxation.

A MR examination is thus made up of a series of pulse sequences. Different tissues (such as fat and water) have different relaxation times and can be identified separately. By using a "fat suppression" pulse sequence, for example, the signal from fat will be removed, leaving only the signal from any abnormalities lying within it.

Spatial encoding of the MRI signal is accomplished through the use of gradients (smaller magnetic fields) which perturb the main magnetic field, and cause hydrogen protons in different locations to precess (move) at slightly different rates. The portion of the gradient coils and the associated current that is perpendicular to the main magnetic field cause a force (Lorentz force) on the coils. The gradients are turned on and off very quickly in this process causing them to vibrate causing the majority of the noise associated with the MRI environment. This still occurs even though they are embedded in an epoxy.

Parameter Weighting

Terms such as "T1-weighted" and "T2-weighted" are among the most overused and least understood concepts in MR imaging. In the broadest sense, these terms are used to communicate to other physicians the type of MR pulse sequence employed to generate a series of images.

Most non-radiologists are often taught to look at the "color" of cerebrospinal fluid (CSF) or other fluids to determine the type of "weighting" — dark CSF means "T1-weighting" and bright CSF means "T2-weighting". Although this simple scheme worked fine in the past, now consider the brain image from the commonly used T2-FLAIR (fluid-attenuated inversion recovery) sequence. This sequence is known to have strong sensitivity to T2 changes, but the CSF signal has been suppressed by an inverting pulse and rendered black. This can lead to confusion for some since parts of "weighting" image has similar coloring to a "FLAIR" image.

A fundamental misconception about "weighting", is that contrast in the image is dominated by one specific tissue parameter to the exclusion of all others. Another common misconception is that T1-weighted or T2-weighted images are parameter "maps" whose pixel intensities are proportional to tissue T1 or T2 values.

It's alright to use terms like "T1-weighted" and "T2-weighted" as long as you realize they are imprecise, are not parameter "maps", and that nearly all images have mixed contributions from all the different tissue parameters.

T1-Weighted Scan Basics

T1-weighted image (also referred to as T1WI or "spin-lattice" relaxation time) is one of the basic pulse sequences in MRI and demonstrates differences in the T1 relaxation times of tissues. This differentiates anatomical structures mainly on the basis of T1 values, for example the scanning parameters are set (short TR/short TE) to minimize T2 relaxation effects.

A T1-weighted image relies upon the longitudinal relaxation of a tissue's net magnetization vector (NMV). Basically, spins aligned in an external magnetic field (Bo) are put into the transverse plane by an RF pulse. They then slide back toward the original equilibirum of the Bo. Not all tissues get back to equilibirum equally quickly, and a tissue's T1 reflects the amount of time its protons' spins realign with the Bo.

Fat quickly realigns its longitudinal magnetization with the Bo, and it therefore appears bright on a T1-weighted image. Conversely, water has much slower longitudinal magnetization realignment after an RF pulse, and therefore has less transverse magnetization after a RF pulse. Thus, water has low signal and appears dark.

If T1-weighted images didn't have short repetition times (TRs), then all the protons would recover their alignment with the main magnetic field and the image would be uniformly intense. Selecting a TR shorter than the tissues' recovery time allows one to differentiate them, such as with tissue contrast.

T1-weighted sequences provide the best contrast for paramagnetic contrast agents such as gadolinium-containing compounds.

A Gadolinium (gd)-Enhanced T1-Weighted Scan Reveals Only New Lesions

These are areas where the disease that are currently active. Before the MRI, an injection of gadolinium (gd) is administered. This will distinguish the active lesions from the normal parts of the brain. When MS is active, gadolinium will cross the blood-brain barrier and reveal areas of inflammation by becoming lighter or brighter. These are called "enhancing lesions" because they are able to be seen.

A gadolinium-enhanced T1-weighted MRI scan supplies information about current disease activity by highlighting areas of breakdown in the blood-brain barrier that indicate inflammation. The blood-brain barrier is a cell layer around blood vessels in the brain and spinal cord that prevents substances from passing out of the blood stream into the central nervous system (CNS). These areas of inflammation appear as active lesions-meaning that they are new, or getting bigger. T1-weighted images also show "black holes," which are thought to indicate areas of permanent damage. T2-weighted MRI scans are used to provide information about disease burden or lesion load or the total amount of lesion area.

Over time, lesions on gd-enhancing MRI may grow or shrink, depending on how active an exacerbation is. This type of MRI will not show older, inactive lesions.

T2-Weighted Scans

T2-weighted scans don't pick up new lesions as well as T1 scans but rather show older, inactive lesions. Regular T2 MRI's are important for tracking long-term disease progression.

T2-weighted scans differentiate anatomical structures mainly on the basis of T2 values, for example the scanning parameters are set (long TR/long TE) to minimize T1 relaxation effects.

Appearance of FLAIR, T1 & T2-Weighted Scans

FLAIR MRI is a heavily T2-weighted technique that dampens ventricular CSF signal. This causes the highest signals on the sequence are from certain brain parenchymal abnormalities, such as MS lesions, while the CSF appears black.

With T1 and T2 scans, the brain will appear to be lighter in the middle and have darker shades surrounding it. Just the opposite will occur with FLAIR scans with the dark areas toward the middle and lighter shades surrounding.

On a T1-weighted scans show tissues with high fat content (such as white matter) appear bright and compartments filled with water (CSF) appears dark. This is good for demonstrating anatomy.

On a T2-weighted scan compartments filled with water (such as CSF compartments) appear bright and tissues with high fat content (such as white matter) appear dark. This is good for demonstrating pathology since most, but not all, lesions (damaged tissue) tend to develop edema and are associated with an increase in water content.

With the addition of an additional RF pulse and additional manipulation of the magnetic gradients, a T2-weighted sequence can be converted to a FLAIR sequence, in which free water is now dark, but edematous tissues remain bright. This sequence in particular is currently the most sensitive way to evaluate the brain for demyelinating diseases, such as MS.

Gd-enhanced T1 and T2-weighted MRIs can depict acute active MS lesions. These appear as enhancing white matter lesions, and the presence of an enhancing lesion has been shown to increase the specificity for MS.

 T1 with Contrast

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 T2 Weighted

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 Flair

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 The Brain and Related Structures in MRI
 Normal T1 T2 Bone Dark black Dark black Air Dark black Dark black Muscle Dark gray Dark gray White matter Light gray Dark gray Gray matter Dark gray Light gray Fat Dark black Very white