MRI sequence


An MRI sequence in magnetic resonance imaging is a particular setting of pulse sequences and pulsed field gradients, resulting in a particular image appearance.
A multiparametric MRI is a combination of two or more sequences, and/or including other specialized MRI configurations such as spectroscopy.

Spin echo

T1 and T2

Each tissue returns to its equilibrium state after excitation by the independent relaxation processes of T1 and T2.
To create a T1-weighted image, magnetization is allowed to recover before measuring the MR signal by changing the repetition time. This image weighting is useful for assessing the cerebral cortex, identifying fatty tissue, characterizing focal liver lesions, and in general, obtaining morphological information, as well as for post-contrast imaging.
To create a T2-weighted image, magnetization is allowed to decay before measuring the MR signal by changing the echo time. This image weighting is useful for detecting edema and inflammation, revealing white matter lesions, and assessing zonal anatomy in the prostate and uterus.
The standard display of MRI images is to represent fluid characteristics in black and white images, where different tissues turn out as follows:
SignalT1-weightedT2-weighted
High
  • More water content, as in edema, tumor, infarction, inflammation and infection
  • Extracellularly located methemoglobin in subacute hemorrhage
    • Inter- mediateGray matter darker than white matterWhite matter darker than grey matter
    Low
  • Bone
  • Urine
  • CSF
  • Air
  • More water content, as in edema, tumor, infarction, inflammation, infection, hyperacute or chronic hemorrhage
  • Low proton density as in calcification
  • Bone
  • Air
  • Fat
  • Low proton density, as in calcification and fibrosis
  • Paramagnetic material, such as deoxyhemoglobin, intracelullar methemoglobin, iron, ferritin, hemosiderin, melanin
  • Protein-rich fluid

    • Proton density

    Proton density - weighted images are created by having a long repetition time and a short echo time. On images of the brain, this sequence has a more pronounced distinction between gray matter and white matter, but with little contrast between brain and CSF. It is very useful for the detection of joint disease and injury.

    Gradient echo

    A gradient echo sequence is the base of many important derived sequences such as echo-planar imaging and SSFP stationary sequences. It allows to obtain very short repetition times, and therefore to acquire images in a short time.
    The gradient echo sequence is characterized by a single excitation followed by a gradient applied along the reading axis called the dephasing gradient. This gradient modifies the spin phase in a spatially dependent manner, so that at the end of the gradient the signal will be completely canceled because the coherence between the spins will be completely destroyed.
    At this point the reading gradient of opposite polarity is applied, so as to compensate for the effect of the disparity gradient. When the area of the reading gradient is equal to that of the mismatching gradient, the spins will have a coherent new phase, and therefore a signal will be detectable again. This signal takes the name of echo or more specifically of gradient echo signal, because it is produced by rephasing due to a gradient.
    The sequences of the gradient echo type allow to achieve very short repetition times, as the acquisition of an echo corresponds to the acquisition of a k-space line, and this acquisition can be made quick by increasing the amplitude of the gradients of rephasing and reading. A sequence of the spin echo type must instead wait for the exhaustion of the signal that is formed spontaneously after the application of the excitation impulse before it can produce an echo.
    For comparison purposes, the repetition time of a gradient echo sequence is of the order of 3 milliseconds, versus about 30 ms of a spin echo sequence.

    Spoiling

    At the end of the reading, the residual transverse magnetization can be terminated or maintained.
    In the first case there is a spoiled sequence, such as the FLASH sequence, while in the second case there are SSFP sequences.

    Steady-state free precession

    Steady-state free precession imaging is an MRI technique which uses steady states of magnetizations. In general, SSFP MRI sequences are based on a gradient-echo MRI sequence with a short repetition time which in its generic form has been described as the FLASH MRI technique. While spoiled gradient-echo sequences refer to a steady state of the longitudinal magnetization only, SSFP gradient-echo sequences include transverse coherences from overlapping multi-order spin echoes and stimulated echoes. This is usually accomplished by refocusing the phase-encoding gradient in each repetition interval in order to keep the phase integral constant. Fully balanced SSFP MRI sequences achieve a phase of zero by refocusing all imaging gradients.
    New methods and variants of existing methods are often published when they are able to produce better results in specific fields. Examples of these recent improvements are T-weighted turbo spin-echo, double inversion recovery MRI or phase-sensitive inversion recovery MRI, all of them able to improve imaging of brain lesions. Another example is MP-RAGE, which improves images of multiple sclerosis cortical lesions.

    In-phase and out-of-phase

    In-phase and out-of-phase sequences correspond to paired gradient echo sequences using the same repetition time but with two different echo times. This can detect even microscopic amounts of fat, which has a drop in signal on OOP compared to IP. Among renal tumors that do not show macroscopic fat, such a signal drop is seen in 80% of the clear cell type of renal cell carcinoma as well as in minimal fat angiomyolipoma.

    Effective T2 (T2* or "T2-star")

    T2*-weighted imaging can be created as a postexcitation refocused gradient echo sequence with small flip angle. The sequence of a GRE T2*WI requires high uniformity of the magnetic field.

    Commercial names of gradient echo sequences

    Inversion recovery

    Fluid-attenuated inversion recovery

    Fluid-attenuated inversion recovery is an inversion-recovery pulse sequence used
    to nullify the signal from fluids. For example, it can be used in brain imaging to suppress cerebrospinal fluid so as to bring out periventricular hyperintense lesions, such as multiple sclerosis plaques. By carefully choosing the inversion time TI, the signal from any particular tissue can be suppressed.

    Turbo inversion recovery magnitude

    Turbo inversion recovery magnitude measures only the magnitude of a turbo spin echo after a preceding inversion pulse, thus is phase insensitive.
    TIRM is superior in the assessment of osteomyelitis and in suspected head and neck cancer. Osteomyelitis appears as high intensity areas. In head and neck cancers, TIRM has been found to both give high signal in tumor mass, as well as low degree of overestimation of tumor size by reactive inflammatory changes in the surrounding tissues.

    Diffusion weighted

    measures the diffusion of water molecules in biological tissues. Clinically, diffusion MRI is useful for the diagnoses of conditions or neurological disorders, and helps better understand the connectivity of white matter axons in the central nervous system. In an isotropic medium, water molecules naturally move randomly according to turbulence and Brownian motion. In biological tissues however, where the Reynolds number is low enough for laminar flow, the diffusion may be anisotropic. For example, a molecule inside the axon of a neuron has a low probability of crossing the myelin membrane. Therefore, the molecule moves principally along the axis of the neural fiber. If it is known that molecules in a particular voxel diffuse principally in one direction, the assumption can be made that the majority of the fibers in this area are parallel to that direction.
    The recent development of diffusion tensor imaging enables diffusion to be measured in multiple directions, and the fractional anisotropy in each direction to be calculated for each voxel. This enables researchers to make brain maps of fiber directions to examine the connectivity of different regions in the brain or to examine areas of neural degeneration and demyelination in diseases like multiple sclerosis.
    Another application of diffusion MRI is diffusion-weighted imaging. Following an ischemic stroke, DWI is highly sensitive to the changes occurring in the lesion. It is speculated that increases in restriction to water diffusion, as a result of cytotoxic edema, is responsible for the increase in signal on a DWI scan. The DWI enhancement appears within 5–10 minutes of the onset of stroke symptoms and remains for up to two weeks. Coupled with imaging of , researchers can highlight regions of "perfusion/diffusion mismatch" that may indicate regions capable of salvage by reperfusion therapy.
    Like many other specialized applications, this technique is usually coupled with a fast image acquisition sequence, such as echo planar imaging sequence.

    Perfusion weighted

    Perfusion-weighted imaging is performed by 3 main techniques:
    The acquired data is then postprocessed to obtain perfusion maps with different parameters, such as BV, BF, MTT and TTP.
    In cerebral infarction, the penumbra has decreased perfusion. Another MRI sequence, diffusion-weighted MRI, estimates the amount of tissue that is already necrotic, and the combination of those sequences can therefore be used to estimate the amount of brain tissue that is salvageable by thrombolysis and/or thrombectomy.

    Functional MRI

    measures signal changes in the brain that are due to changing neural activity. It is used to understand how different parts of the brain respond to external stimuli or passive activity in a resting state, and has applications in behavioral and cognitive research, and in planning neurosurgery of eloquent brain areas. Researchers use statistical methods to construct a 3-D parametric map of the brain indicating the regions of the cortex that demonstrate a significant change in activity in response to the task. Compared to anatomical T1W imaging, the brain is scanned at lower spatial resolution but at a higher temporal resolution. Increases in neural activity cause changes in the MR signal via T changes; this mechanism is referred to as the BOLD effect. Increased neural activity causes an increased demand for oxygen, and the vascular system actually overcompensates for this, increasing the amount of oxygenated hemoglobin relative to deoxygenated hemoglobin. Because deoxygenated hemoglobin attenuates the MR signal, the vascular response leads to a signal increase that is related to the neural activity. The precise nature of the relationship between neural activity and the BOLD signal is a subject of current research. The BOLD effect also allows for the generation of high resolution 3D maps of the venous vasculature within neural tissue.
    While BOLD signal analysis is the most common method employed for neuroscience studies in human subjects, the flexible nature of MR imaging provides means to sensitize the signal to other aspects of the blood supply. Alternative techniques employ arterial spin labeling or weighting the MRI signal by cerebral blood flow and cerebral blood volume. The CBV method requires injection of a class of MRI contrast agents that are now in human clinical trials. Because this method has been shown to be far more sensitive than the BOLD technique in preclinical studies, it may potentially expand the role of fMRI in clinical applications. The CBF method provides more quantitative information than the BOLD signal, albeit at a significant loss of detection sensitivity.

    Magnetic resonance angiography

    is a group of techniques based to image blood vessels. Magnetic resonance angiography is used to generate images of arteries in order to evaluate them for stenosis, occlusions, aneurysms or other abnormalities. MRA is often used to evaluate the arteries of the neck and brain, the thoracic and abdominal aorta, the renal arteries, and the legs.

    Phase contrast

    Phase contrast MRI is used to measure flow velocities in the body. It is used mainly to measure blood flow in the heart and throughout the body. PC-MRI may be considered a method of magnetic resonance velocimetry. Since modern PC-MRI typically is time-resolved, it also may be referred to as 4-D imaging.

    Susceptibility weighted imaging

    Susceptibility-weighted imaging is a new type of contrast in MRI different from spin density, T1, or T2 imaging. This method exploits the susceptibility differences between tissues and uses a fully velocity compensated, three dimensional, RF spoiled, high-resolution, 3D gradient echo scan. This special data acquisition and image processing produces an enhanced contrast magnitude image very sensitive to venous blood, hemorrhage and iron storage. It is used to enhance the detection and diagnosis of tumors, vascular and neurovascular diseases, multiple sclerosis, Alzheimer's, and also detects traumatic brain injuries that may not be diagnosed using other methods.

    Magnetization transfer

    Magnetization transfer is a technique to enhance image contrast in certain applications of MRI.
    Bound protons are associated with proteins and as they have a very short T2 decay they do not normally contribute to image contrast. However, because these protons have a broad resonance peak they can be excited by a radiofrequency pulse that has no effect on free protons. Their excitation increases image contrast by transfer of saturated spins from the bound pool into the free pool, thereby reducing the signal of free water. This homonuclear magnetization transfer provides an indirect measurement of macromolecular content in tissue. Implementation of homonuclear magnetization transfer involves choosing suitable frequency offsets and pulse shapes to saturate the bound spins sufficiently strongly, within the safety limits of specific absorption rate for MRI.
    The most common use of this technique is for suppression of background signal in time of flight MR angiography. There are also applications in neuroimaging particularly in the characterization of white matter lesions in multiple sclerosis.

    Fast spin echo

    Fast spin echo, also called turbo spin echo is a sequence that results in fast scan times. In this sequence, several 180 refocusing radio-frequency pulses are delivered during each echo time interval, and the phase-encoding gradient is briefly switched on between echoes.
    The FSE/TSE pulse sequence superficially resembles a conventional spin-echo sequence in that it uses a series of 180º-refocusing pulses after a single 90º-pulse to generate a train of echoes. The FSE/TSE technique, however, changes the phase-encoding gradient for each of these echoes. As a result of changing the phase-encoding gradient between echoes, multiple lines of k-space can be acquired within a given repetition time. Because of multiple phase-encoding lines are acquired during each TR interval, FSE/TSE techniques may significantly reduce imaging time.

    Fat suppression

    Fat suppression is useful for example to distinguish active inflammation in the intestines from fat deposition such as can be caused by long-standing inflammatory bowel disease, but also obesity, chemotherapy and celiac disease. Techniques to suppress fat on MRI mainly include:
    This method exploits the paramagnetic properties of neuromelanin and can be used to visualize the substantia nigra and the locus coeruleus. It is used to detect the atrophy of these nuclei in Parkinson's disease and other parkinsonisms, and also detects signal intensity changes in major depressive disorder and schizophrenia.

    Uncommon and experimental sequences

    The following sequences are not commonly used clinically, and/or are at an experimental stage.

    T1 rho (T1ρ)

    T1 rho is an experimental MRI sequence that may be used in musculoskeletal imaging. It does not yet have widespread use.
    Molecules have a kinetic energy that is a function of the temperature and is expressed as translational and rotational motions, and by collisions between molecules. The moving dipoles disturb the magnetic field but are often extremely rapid so that the average effect over a long time-scale may be zero. However, depending on the time-scale, the interactions between the dipoles do not always average away. At the slowest extreme the interaction time is effectively infinite and occurs where there are large, stationary field disturbances. In this case the loss of coherence is described as a "static dephasing". T2* is a measure of the loss of coherence in an ensemble of spins that includes all interactions. T2 is a measure of the loss of coherence that excludes static dephasing, using an RF pulse to reverse the slowest types of dipolar interaction. There is in fact a continuum of interaction time-scales in a given biological sample, and the properties of the refocusing RF pulse can be tuned to refocus more than just static dephasing. In general, the rate of decay of an ensemble of spins is a function of the interaction times and also the power of the RF pulse. This type of decay, occurring under the influence of RF, is known as T1ρ. It is similar to T2 decay but with some slower dipolar interactions refocused, as well as static interactions, hence T1ρ≥T2.

    Others