MRI sequence

An MRI sequence in magnetic resonance imaging (MRI) 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 (spin-lattice; that is, magnetization in the same direction as the static magnetic field) and T2 (spin-spin; transverse to the static magnetic field).
To create a T1-weighted image, magnetization is allowed to recover before measuring the MR signal by changing the repetition time (TR). 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 (TE). 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:
Proton density.
Proton density (PD)- weighted images are created by having a long repetition time (TR) and a short echo time (TE). On images of the brain, this sequence has a more pronounced distinction between gray matter (bright) and white matter (darker gray), 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 (TR), 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 (except for the effects of T2* relaxation), 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 (unlike the spin echo signal whose rephasing is due to a radiofrequency pulse).
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 (free induction decay).
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 (through the application of suitable gradients and the excitation through pulses with a variable phase radiofrequency) or maintained.
In the first case there is a spoiled sequence, such as the FLASH (Fast Low-Angle Shot) sequence, while in the second case there are SSFP (Steady-state free precession imaging) sequences.
Steady-state free precession.
Steady-state free precession imaging (SSFP MRI) is an MRI technique which uses steady states of magnetizations. In general, SSFP MRI sequences are based on a (low flip angle) 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 (magnetizations) 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 (or gradient moment) 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 ("T"2 TSE MRI), double inversion recovery MRI (DIR-MRI) or phase-sensitive inversion recovery MRI (PSIR-MRI), all of them able to improve imaging of brain lesions. Another example is MP-RAGE (magnetization-prepared rapid acquisition with gradient echo), which improves images of multiple sclerosis cortical lesions.
In-phase and out-of-phase.
In-phase (IP) and out-of-phase (OOP) sequences correspond to paired gradient echo sequences using the same repetition time (TR) but with two different echo times (TE). 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.
Inversion recovery.
Fluid-attenuated inversion recovery.
Fluid-attenuated inversion recovery (FLAIR) 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 time between the inversion and excitation pulses), the signal from any particular tissue can be suppressed.
Turbo inversion recovery magnitude.
Turbo inversion recovery magnitude (TIRM) 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.
Diffusion MRI measures the diffusion of water molecules in biological tissues. Clinically, diffusion MRI is useful for the diagnoses of conditions (e.g., stroke) or neurological disorders (e.g., multiple sclerosis), and helps better understand the connectivity of white matter axons in the central nervous system. In an isotropic medium (inside a glass of water for example), 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 (DTI) 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 (using tractography) or to examine areas of neural degeneration and demyelination in diseases like multiple sclerosis.
Another application of diffusion MRI is diffusion-weighted imaging (DWI). Following an ischemic stroke, DWI is highly sensitive to the changes occurring in the lesion. It is speculated that increases in restriction (barriers) to water diffusion, as a result of cytotoxic edema (cellular swelling), 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 (as compared to computed tomography, which often does not detect changes of acute infarct for up to 4–6 hours) and remains for up to two weeks. Coupled with imaging of cerebral perfusion, 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" (PWI) is performed by 3 main techniques:
The acquired data is then postprocessed to obtain perfusion maps with different parameters, such as BV (blood volume), BF (blood flow), MTT (mean transit time) and TTP (time to peak).
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.
Functional MRI (fMRI) 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 (typically once every 2–3 seconds). Increases in neural activity cause changes in the MR signal via "T" changes; this mechanism is referred to as the BOLD (blood-oxygen-level dependent) 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 (ASL) or weighting the MRI signal by cerebral blood flow (CBF) and cerebral blood volume (CBV). 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.
Magnetic resonance angiography ("MRA") is a group of techniques based to image blood vessels. Magnetic resonance angiography is used to generate images of arteries (and less commonly veins) in order to evaluate them for stenosis (abnormal narrowing), occlusions, aneurysms (vessel wall dilatations, at risk of rupture) 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 (the latter exam is often referred to as a "run-off").
Phase contrast.
Phase contrast MRI (PC-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 (three spatial dimensions plus time).
Susceptibility weighted imaging.
Susceptibility-weighted imaging (SWI) is a new type of contrast in MRI different from spin density, "T"1, or "T"2 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 (stroke and hemorrhage), multiple sclerosis, Alzheimer's, and also detects traumatic brain injuries that may not be diagnosed using other methods.
Magnetization transfer.
Magnetization transfer (MT) 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 (FAISE or FSE, ref 65bis), also called turbo spin echo (TSE) is a sequence that results in fast scan times. In this sequence, several 180 refocusing radio-frequency pulses are delivered during each echo time (TR) interval, and the phase-encoding gradient is briefly switched on between echoes.
The FSE/TSE pulse sequence superficially resembles a conventional spin-echo (CSE) 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 (a conventional multi-echo sequence collects all echoes in a train with the same phase encoding). As a result of changing the phase-encoding gradient between echoes, multiple lines of k-space (i.e., phase-encoding steps) can be acquired within a given repetition time (TR). Because of multiple phase-encoding lines are acquired during each TR interval, FSE/TSE techniques may significantly reduce imaging time.
65-bis - Ph. MELKI, R.V. MULKERN, L.P. PANYCH, F.A. JOLESZ. 
Comparing Spin Echo Sequences with the FAISE Method. 
J. Magn. Reson. Imag. 1991; 1:319-326. 
65-Ter Ph. MELKI, F.A. JOLESZ, R.V. MULKERN. 
Partial RF echo planar with the FAISE method: Experimental and theoritical assessment of image artifacts. 
Mag. Res. Med. 1992; 26:328-341.
65-Quatro - Ph. MELKI, F.A. JOLESZ, R.V. MULKERN. 
Partial RF echo planar imaging with the FAISE method: Contrast equivalence with spin echo sequences. 
Mag. Res. Med. 1992; 26:342-354.
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 (but possibly inactive) inflammatory bowel disease, but also obesity, chemotherapy and celiac disease. Techniques to suppress fat on MRI mainly include:
Neuromelanin imaging.
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 (T1ρ) 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 (e.g., a metallic implant). 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 (including static dephasing). 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.