Fat Suppression

Suppression of fat signal is used in MRI images when the fat signal causes artefacts or otherwise obscures a tissue of interest.

There are a number of fat suppression methods. Which one you choose depends on the pros and cons of each technique. These change with field strength, field-of-view size, whether regional or global fat suppression is required, whether an increase in scan time is acceptable, etc. Additionally, the absolute quality of fat suppression may not motivate the choice of technique; contrast between tissues of interest may be more important. Overall SNR in an image may also be a deciding factor.

Here is a brief summary of fat suppression techniques.

Short inversion-Time Inversion Recovery

Short inversion-Time Inversion Recovery (STIR) employs a 180° inversion pulse to invert all magnetisation. Then imaging proceeds after a delay, when the longitudinal recovery of fat magnetisation has reached the null point, when there is no fat magnetisation to flip into the x-y plane. Tissues with a T1 relaxation time different to fat have a signal, because they either have not yet reached the null point, or have recovered past it. Most tissues recover more slowly than fat, and so a STIR images have intrinsically lower SNR. Care has to be taken in interpretation of contrast between tissues because of the incomplete relaxation of the water signal of tissues when the image is acquired.

STIR is often preferred when spectrally-selective techniques may not be ideal (large fields-of-view, lower field strengths, areas of high magnetic susceptibility), and the necessary inclusion of the inversion time (TI) to null fat increases scan time. Note that STIR is based on the difference in T1 relaxation times between water and lipid, not their chemical shift. If the inversion pulse is is adiabatic, STIR also becomes insensitive to B1 inhomogeneity.

Spectrally-Selective RF Pulses

RF pulses are tailored to excite protons in a particular resonant frequency range. This range can be narrowed so that the RF pulse affects only water, or only fat (unlike STIR, where all magnetisation gets inverted). This works better at higher field strengths where these resonant frequencies are more separated. Good magnet (B0) homogeneity is required to make this frequency-selective excitation effective, and so techniques based on frequency-selective excitation are more effective over smaller fields-of-view. In general, this technique is called CHESS (CHEmical Shift Selective). If an excitation pulse is water-only, fat may be considered “suppressed” by dint of it being left alone.

A fat-selective CHESS RF pulse can be used as a preparation pulse. After a delay, when the longitudinal recovery of fat magnetisation passes throught the null point, MR image acquisition can occur such that minimal signal from fat contributes to the image. This technique is called SPECIAL (SPECtral Inversion At Lipid). The RF preparation-pulse angle can be reduced to closer to 90° so that the inversion time is as short as possible, which saves imaging time. In this way the preparation pulse is more like a saturation pulse (and “inversion” is a slight misnomer). This is called SPIR (Spectral Presaturation with Inversion Recovery), or on some systems simply “Fat SAT”.

If the RF pulse is adiabatic, making it insensitive to B1 (flip angle) inhomogeneity, a full 180° pulse is used, followed by spoiler gradients which ensure any magnetisation in the transverse plane is dephased. Then MR excitation for data acquisition occurs after a delay (longer than that of SPIR) to allow fat to reach its null point. This is called SPAIR (SPectral Attenuated Inversion Recovery).

Composite RF Pulses

Composite RF pulses can be used to produce a signal from only water protons by making use of the dephasing of fat and water. They are RF pulses made up of a series of shorter RF pulses with small delays between them. They can be quite complicated, but here is a simple example to explain the method.

First, a 45° excitation pulse flips both fat and water. Then after a short time, fat and water are exactly out of phase (both still at 45°, but with opposing transverse components of magnetisation, and thus have a 90° angle between them). Another 45° RF pulse is then applied which flips the fat net magnetisation back to Mz, and puts the water magnetisation in the x-y plane, providing a fat-suppressed signal. This method of fat suppression does not depend on the frequency separation of fat and water (good for low field MR where that separation is small) and is relatively insensitive to B1 non-uniformity (good for high field MR where B1 uniformity is more challenging), but it is sensitive to B0 inhomogeneity. One implementation of this method is called ProSet (PRinciple Of Selective Excitation Technique).

Regional Saturation Bands

Regional saturation employs a 90° RF pulse which, when combined with a gradient orthogonal to the imaging plane, affects only a part of the field-of-view. If imaging follows immediately, no signal will be returned from the suppressed region, since there is no longitudinal magnetisation available to receive the RF excitation pulse. It can be used: to suppress fat within regions of images where the fat signal obscures a tissue of interest; to mitigate aliased signals into a region-of-interest; to reduce the effects of chemical shift displacement of signal in volume selection; or to define the region of interest itself by suppressing surrounding signals (especially in MR spectroscopy). The saturation bands are called REST slabs (REgional Saturation Technique), Presat or SAT bands.

Slice-Selective Gradient Reversal

Slice-selective gradient reversal (SSGR) is possible in spin-echo based sequences, and is appropriate at higher field when chemical shift between fat and water is larger. SSGR relies on through-plane chemical shift being in opposite directions for the 90° and the 180° pulses, so that the shifted fat doesn’t receive both RF pulses and therefore no spin echo is formed from the fat. This is achieved by inverting the polarity of the slice selection gradient associated with the 180° refocusing pulse. SSGR is effective over large fields-of-view and may be combined with other methods of fat suppression above.


Dixon’s method relies on acquiring images at carefully chosen echo times and using pixel-by-pixel image algebra to calculate a “water only” or “fat only” image. DIXON methods differ from the other methods described in this post in that they postpone the water and fat separation until reconstruction. In this way some of the drawbacks of the other methods are avoided.

Here is the basic idea. Two images are acquired, one at a TE when fat and water are in-phase, and another when fat and water are out-of-phase. Then a water-only image can be calculated using (Image1+Image2)/2. In its most basic form the technique is straightforward, but in practice to make it work a number of non-trivial extensions to the basic technique are required both in data acquisition and in the calculation of water-only or fat-only images. This is because the basic method assumes perfect B0 homogeneity (which is not possible in the presence of a patient), complete absence of eddy currents, negligible susceptibility effects, and it does not account for variation in echo amplitudes. The extensions to the basic method account for these false assumptions.

DIXON-based fat suppression can be very effective in areas of high magnetic susceptibility, where other techniques fail. Note that the TEs are usually fixed in order to make the method work, and so it is not an add-on method for other sequences.

Magnetisation transfer based

A recently reported technique relies on magnetisation transfer (MT). A brief recap of MT follows.
As you know, radiofrequency (RF) excitation pulses have to be at the Larmor frequency of the hydrogen atom (1H): on resonance. What you may not know is that in MRI we use 1H in free water molecules; other water molecules are around, such as those attached to macromolecules and membranes (we call these 1H bound or restricted). These other 1H have a very large range of Larmor frequencies and have such a short T2 relaxation time (less than 1ms, due to their restricted mobility) that they are not visible in MR images. We can excite or saturate some of the bound water protons by applying an RF pulse off-resonance (i.e. not on the resonant frequency of free water). Then the magnetisation of these bound protons is transferred to the free 1H protons and the free 1H behave as if they have received some of the off-resonance RF pulse directly. This magnetisation exchange is called magnetisation transfer (MT). MT is usually used to provide another contrast mechanism because the effect of MT varies between tissues; if we saturate the bound/restricted 1H , varying amounts of saturation occurs in the free 1H of tissues.

So back to the fat suppression method. It’s a simple image subtraction of an image with presaturation of both tissue protein and membrane phospholipid protons, from an image without presaturation. In the with-saturation image, efficient MT between water and tissue protein and membrane phospholipid means water gets saturated too, yielding an almost fat-only image. Subtract this from a regular image and you get a water-only image. The nice thing about this method is that fat signals are removed irrespective of their chemical shift (of which there is a range in vivo). It’s also not affected by B0 or B1 inhomogeneity. There is a small reduction of signal from water because not all the water gets saturated via MT, though in most tissues the eventual water signal-loss is small. A downside of the technique is a twofold increase in scan time, and possible misregistration between the two images before subtraction.

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