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Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Sunday, January 29, 2012

Common persistent EPI artifacts: Abnormally high N/2 ghosts (1/2)

In this and a subsequent post I am going to cover some common situations when the N/2 ghosts can become abnormally high, i.e. higher than it is possible to achieve with comparatively small tweaks to the setup. For now I am going to restrict the discussion to temporally static, or persistent, ghosts. Furthermore, I will restrict the discussion to situations over which you can exert some control, usually through the subject setup and via EPI parameter selection. I'll cover the origins of dynamic ghosts later on in this series, once you've got a better grasp of the common persistent ghosting sources and are in a position to differentiate between a source that is intermittent and a (persistent) ghost that is being modulated by subject motion.

Before we get into the different experimental conditions that can lead to abnormally high ghosting, it is important that you are familiar with the reason why N/2 ghosts arise in EPI in the first place. So, if the following section sounds like Swahili (and you don't ordinarily speak Swahili) then I would encourage you to spend twenty minutes reviewing the section on N/2 ghosts in PFUFA Part Twelve before continuing here.

Origins of N/2 ghosts: review

Anything that causes a zigzag offset between the odd and even lines of the phase encoding dimension of k-space will lead to an N/2 ghost. Typically, one strives to minimize the zigzag at source, e.g. via shimming, and then a software tweak is applied (using navigator echoes) to clean up the residue as far as possible. The navigator echoes (Siemens uses three) are acquired immediately prior to the EPI readout (the 2D k-space). A phase correction term is derived from the navigator echoes and this term is applied to the k-space prior to 2D FT to reduce the zigzag phase differences. A successful correction is thus dependent on a good match between the phase offset obtained from the navigator echoes and the zigzag through the echo train. Discrepancies will lead to uncorrected ghosting.

There can be many reasons why the navigators don't capture accurately the zigzag across k-space. For example, the navigator echoes measure phase discontinuities arising over just 1-2 milliseconds whereas the echo train takes 20-30 milliseconds to play out. Physical effects that lead to phase evolution over the longer timescale of the echo train won't be corrected - because they won't have been measured - by the navigator echoes. However, it's not essential to understand exactly how the navigator echoes might not be able to capture the phase evolution across k-space. Instead, we can simply take an empirical approach and assess situations when the ghosting is higher than compared to some normal, or best case, level. It's then clear that the navigator echo correction was insufficient, and we should seek to eliminate or reduce the source of the phase difference.

Categorizing the origins of persistent N/2 ghosts

There are several sources of persistent ghosts that can arise from poor scanner installation or tuning, e.g. from gradient calibration errors, or from residual eddy currents. As a general rule there is little that you, as an experimenter, can do to affect these sources. These are issues for your facility physicist and your service engineer. So, from this point forward I'm going to focus attention on the factors that you have at least partial control over. Thus, for simplicity I will assume that your scanner has been installed correctly and is working nominally (as they say at NASA). The question, then, is whether you're doing everything properly. (Siemens users, see Note 1.)

As this is a blog dedicated to improving experimental techniques I am going to organize the different ghost origins along a couple of practical lines. I'll separate the effects that can be attributed to the specifics of the subject and/or the way the subject is oriented in the magnet, from those that are essentially "scanner misuse" effects. The scanner-specific effects would be seen in EPIs of a phantom whereas the subject-specific effects might require a human head to manifest themselves. This distinction is purely to assist you in making appropriate diagnostics should you (I mean when you) encounter an unexpectedly high ghost level.

Finally, while this post will focus on temporally stable ghosts, it is useful to consider the degree of temporal stability for some of the effects we'll see below. Note, however, that this can be a rather artificial distinction when considering brain data because any movement whatsoever of the subject will couple with the root cause of a major ghost and render it temporally unstable to some extent! It is thus important to recognize that in real situations the distinction between "persistent" and "intermittent" may itself be in flux. If you want me to be pedantic then I'm saying the origins of the different effects we'll consider here are temporally constant, or persistent. Later on in this series I will consider sources of ghosting that will vary temporally whether your subject is moving or not. At that point you'll have a complete overview of common ghost sources and you should be able to formulate a systematic approach to diagnosis, and remediation.

Global or local effects?

As was emphasized in Note 5 of PFUFA Part Twelve, the spatial distribution of ghosts may be global (e.g. a badly calibrated on-resonance adjustment due to scanner heating) or local (e.g. regions of high magnetic susceptibility in the frontal lobes) relative to your subject's head and to the EPI slices across it. Put another way, every single slice may exhibit essentially the same bad ghosting or you may just see some regions affected in just one or a few slices. In what follows I will do my best to suggest when an effect is more likely to be global than local, but bear in mind that there may not be a clear distinction in practice. It all depends what's screwed up and how.

Subject-dependent conditions:

Asymmetric orientation of the subject's head leading to a poor shim

GLOBAL - likely to affect all slices to some extent.

Talk about a bad way to start your session. You're in a hurry, already watching the clock, so you rush getting the subject onto the patient bed, ram a couple of pieces of foam down the sides of the subject's head, pop on the top of the head coil and it's go time!

Slow down! Take a moment to check that the bridge of the subject's nose is pointed towards top dead center of the magnet and try to ensure, as best you can by eye, that the head isn't yawed or rotated relative to his looking directly ahead. (Another clue might be that the subject reports not being able to see all of the display, e.g. a coil-mounted mirror.) If you don't you may find that you have to waste more time by repacking the subject's head once you discover that the scanner can't shim the head properly. (See Note 2.) The lower the axes and planes of symmetry through your subject's brain, the harder you have just made it for the shimming algorithm to find a good solution that will maximize brain signal and minimize N/2 ghosts.

In the left image below the subject's head was positioned symmetrically in the magnet, resulting in low ghosts for all EPIs because the shim was good. On the right, the same subject was placed in the magnet with a 5-10 degree rotation. (The subject rotated his head to look to his left very slightly.) A new shim was performed, then the EPI slices were prescribed across the brain to match those in the first case. (This has the effect of nullifying the rotation of the head in the magnet reference frame, so you no longer see the rotation in the images.) At first glance these new EPIs look acceptable, until you compare the ghost level to the left-hand image. As always, I've brought the background intensity up to highlight the ghosts:

Left: good ghost level resulting from the head placed symmetrically in the magnet, i.e. following a good shim. Right: poor ghost level arising from head rotation and a poor shim.
(Do not adjust your set! Yeah, I managed to change the volume on my Mac while I was doing a timed screen shot. Oh well.)

Distortion and dropout would also likely be higher for the rotated head, too. But the more useful diagnostic - the thing that tells you to STOP and check the subject's head orientation, is the high degree of ghosting.

Why is the ghosting higher when the head is rotated? There are usually only eight shim terms on your scanner, three with linear spatial dependence (X, Y, Z) and five with second-order spatial dependence (e.g. Z2, XZ, YZ, XY, X2-Y2) in the magnet frame of reference. The magnetic field across a brain is being affected by venous sinuses, skull, ear cavities, etc. and you are trying to minimize the variation with a low number of spatial terms. Those shims that act with an X and/or Y dependence are operating across the magnet bore, with X being left-right and Y being up-down on most scanners. (See Note 6 in PFUFA Part Seven for a typical magnet frame of reference.) The best combination of shim terms is computed from a field map. It's a tough problem to begin with, having so few shims and such a complex magnetic field. Reducing the already low intrinsic symmetry makes it harder still to compute a good solution to the field map, and reduced magnetic field homogeneity is the result. This leads to bigger k-space offsets and higher ghosting (amongst other things) in EPI.

Poor shim as a result of subject motion during/immediately after shimming

GLOBAL - likely to affect all slices to some extent.

Even when you're careful setting up your subject and you get a good initial shim, the subject may well be working against you! A sneeze or perhaps adjusting body position for comfort can easily displace the subject's head from the initial, well-shimmed position.

In the following figure the images on the left were acquired immediately following a good shim with the head placed symmetrically, and on the right is the result of a head rotation following the shim (with the subject now stationary in the new position) :

(Click to enlarge.)

The slice prescription wasn't changed so you can see clearly the rotation of the brain in addition to the higher ghost level on the right. These twin observations are your cue to have the subject return his head to the starting position (or you'd go do it for him) and re-shim. (Siemens users, see Note 3 in the post, Tactical approaches to (re)shimming for the procedure to trigger a re-shim at any point during a scan session.) A less sophisticated user might just re-acquire a localizer scan and redefine the slice prescription. That would ensure the brain coverage is as desired, but note that the shim is still sub-optimal and therefore the ghost level will remain high. You'll have to take my word for this, I'm afraid I didn't think to acquire a second set of EPIs with a straight prescription. I can guarantee that the ghost level would not change much!

Any time during an fMRI experiment, if you know or suspect that the subject has moved his head since the (last) shim was performed, do another shim! Whether or not you interrupt the session to realign the subject's head is up to you. I would reposition the subject's head only for large deviations that lead to ghosting that isn't fixed by a new shim. Re-shimming is fast - 30-40 seconds - and does no harm even if it doesn't generate a massive benefit, e.g. because the rotation was small enough not to perturb the shim significantly.

Presence of FOD or an implant causing a poor shim

LOCAL - will usually affect some slices more than others.

This one's on you again: pilot error. You can't blame the subject, not even if she forgot to take that last hair clip out. (Well, you could try, but in my lab you're in charge of screening, not the subject!)

In this example I used a spherical gel-filled phantom against which I placed a small push-pin; low-grade steel with a plastic top. The steel pin is about 15 mm long and about 1 mm in diameter. It is considerably smaller than most hair clips but might contain a similar amount of metal to some types of "scrunchie" or metallic hair band. Here's what it does to what should be rather circular slices through a spherical phantom:

(Click to enlarge.)

It should be obvious that the presence of the FOD (foreign object/debris) is massively disrupting the local magnetic field homogeneity here, leading to extreme ghosting amongst other things. Indeed, you could argue that the ghosting is the least of your worries! You've got a rather large hole (dropout) accompanied by some bizarre distortions.

The particular combination of ghosting, dropout and distortion will obviously depend on the size and composition of the conductive foreign object, as well as its location in/near the subject's head. (In an earlier post on FOD I described a couple of incidents when subjects had "missing brain.") You might also see a diffuse effect on ghosting, e.g. because of the presence of a conductive hair product or hair coloring. Or it could be multiple focal effects, as I have seen before with wigs. (You should screen for wigs, by the way!)

If the artifact is the result of an implant that somehow got through screening, e.g. a metal plate in a cheek bone, then it's nearly impossible to tell what the effect(s) will be on the resulting EPI ahead of time. Now, on occasion you might have a valuable subject who has, say, a titanium screw in his upper jaw. Assuming you can't easily replace him, and you've suitably assessed the safety risks, my usual approach is to run a quick pilot session and assess the EPI quality (including the TSNR) before wasting time with subject training, etc. I take a similar approach to subjects with a large number of metal amalgam fillings, especially in the upper jaw.

Next post: Scanner-dependent conditions leading to abnormally high (persistent) N/2 ghosts.



1.  The magnitude and temporal (in)stability of the ghosts may have an RF coil dependence. In this post all data were acquired with the standard 12-channel head coil on a Trio/TIM system. I will deal with the 32-channel head coil in a dedicated post. It turns out that the 32-channel coil isn't a TIM coil and this can lead to different ghost behavior than for the 12-channel coil.

2.  Another likely consequence of hasty subject setup is subject discomfort. The subject's very first position on the patient bed is unlikely to be his most comfortable one. Give your subjects time to make small adjustments before inserting them into the magnet, otherwise you're very likely to find that the subject will make these adjustments anyway - during the scan. Best case, there might not be any significant effect if the subject moves between EPI runs and manages to keep his head in the same position. Or, worst case, you might end up with a restless subject who seeks comfort throughout the runs, trashing your experiment with excessive motion. All because you didn't want to "waste" a couple of minutes at the start of the session getting the subject positioned comfortably and correctly.


  1. Hi there. The description of these artifacts is really interesting but I was wondering if it has already been described in literature, in particular the orientation influence on the ghost level?
    Thank you.

  2. Hi Anon, I'm sure all of these sources have been addressed somewhere in the literature. That said, most of the newer (last ten years) references concern schemes to tackle the ghosts rather than the sources themselves. But I would think that older EPI references, perhaps those from the 80s and 90s when several groups were battling to make hardware acquire EPI at all, might have mention of them. (Incidentally, the recent historical review article on EPI and fMRI by Mark Cohen and Franz Schmitt, is entertaining reading!)

    I just did a very quick pubmed search and couldn't find any review articles. If you need a particular issue referenced, e.g. for an article you're writing, then let me know and I'll try to refine my search.

  3. Nice post! All of these little things can make the difference between good and really bad data. Berkeley Neuroscience is lucky to have you looking out for them.