The 3 T gets a new home

After a very long wait that spanned two prefabricated buildings - we weren't supposed to call them trailers, some sort of negative connotation - the Henry H. Wheeler, Jr. Brain Imaging Center took its first step into a permanent home yesterday with the move of the BIC's existing 3 T Siemens Trio scanner into one of the magnet bays in Li Ka Shing Center for Biomedical and Health Sciences (LKS). With space for two 3 T MRIs, a 7 T MRI, a MEG and a host of functional support facilities, including TMS and EEG prep rooms as well as mechanical and electrical workshops, there will be quite a lot of moving in to be done over the years ahead. For the time being, however, the task is to get the very busy Trio back up and scanning as quickly as possible. Here are a few pictorial and video highlights of the magnet move, with a couple of interesting and hopefully educational features indicated.

The magnet had been ramped down a week before, allowing a lot of preparatory work disconnecting cables and getting access to the removable roof section above the scanner's old home. In this photo you can see the copper foil of the removable roof section, a component of the scanner's Faraday shield (to reject external RF):

The removable roof section was lifted out by crane:

Then the magnet, weighing some 32,000 lbs with the patient table sled attached and the cryostat full of liquid helium, was lifted out and staged in an adjacent parking lot:

Common intermittent EPI artifacts: Subject movement

More fMRI experiments are ruined by subject motion than any other single cause. At least, that is my anecdotal conclusion from a dozen years' performing post-acquisition autopsies on "bad" data. The reasons for this vulnerability are manifold, starting with the type of subjects you're trying to scan. You may be interested in people for whom remaining still is difficult or impossible without sedation of some kind.

However, I think there is another reason why many (most?) fMRIers end up with more subject motion than is practicable: they haven't taken the time to think through the different ways that subjects can thwart your best efforts. In other words, what we are considering is largely experimental technique, or bedside manner as medical types refer to this stuff.

With the possible (and debatable) exception of bite bars, which aren't popular for myriad reasons, there is no panacea for motion. Why? As we shall see, it's not just movement of the head that's a concern. You need to consider a subject's comfort, arousal level, propensity to want to breathe, and many other things that might be peripheral to your task but are very much on the mind of your (often fMRI-naive) subjects.

Now, before we get any farther I need to outline what this post will cover, and what it won't. The focus of this post is on single-shot, unaccelerated gradient echo EPI - the sort of plain vanilla sequence that the majority of sites use for fMRI. I won't be covering the effects of motion on parallel imaging such as GRAPPA, for example. I will also restrict discussion here to the effects of motion on axial slices. Hopefully you can extrapolate to different slice prescriptions. But, rest assured that this isn't the last word in motion, not by a long chalk. Motion has come up before on this blog, e.g. in relation to GRAPPA for EPI, and the ubiquity of the problem implies that the issue will arise in many subsequent posts, too. Take today's post as an introduction to the general problem.

My final caveat on the utility of today's post. As this blog is focused on practical matters I will restrict the bulk of the discussion to things that you'll see and can control online, in real time. There are many tools that can be used to provide useful diagnostics post hoc, some of which I will mention. But this isn't a post aimed at showing you what went wrong. Rather, the intent of this post is to describe what is going wrong, such that you might be able to intercede and fix the situation. Some sites have useful real-time diagnostics that can tell you when (and perhaps how) a subject is moving, but they aren't widespread. Thus, for today's post we shall keep things simple and restrict the discussion to what can be seen in the EPIs themselves, as they are acquired.

WARNING: If you haven't run an fMRI experiment in a while then you might want to stop reading this post here and go and review the earlier post, Understanding fMRI artifacts: "Good" axial data. That post highlights our target: the low motion case.


Eye movements

Let's start simply. Here is a video of a subject intentionally moving his eyes to a target. Saccading is the technical term, I hear. (See Note 1 for experimental details. Parameters were fixed throughout for this post, unless mentioned to the contrary in any section below.) There are twenty volumes played back at a rate of 5 frames/sec:

Rare intermittent EPI artifacts: Spiking, sparking and arcing

 
Whatever you call them - spikes, sparks or arcs - the presence of unwanted electrical discharges during data acquisition can have a dramatic effect on the appearance of your EPIs and will likely result in poor or unusable data. (See Note 1.) There are many potential sources of unwanted electrical discharges - what I shall refer to as spikes for the rest of this post, regardless of the origin - in and around an MRI scanner. They can arise from within the scanner itself, or from items in the magnet room, or from items of clothing on a subject who hasn't been screened quite as thoroughly as he might have been.

Before we get to the sources, however, let's take a look at what we're talking about. Take a look at this mosaic of EPIs:

See the problem? No? Exactly! As I have mentioned several times in the past, many artifacts are best (or only) seen once the background level is brought up. Like this:

Aha! We clearly see the artifacts in this view: strange, variable patterns across entire slices.

Now, it isn't always necessary to crank the background intensity up to be able to see the effects of spikes, as we will see below. But as a general rule, the very first signs of spiking will be quite subtle and will likely be hidden away down in the noise with the N/2 ghosts and all the other crud. This is when you want to catch them, before they become intense and wreck your experiment. So, just to reinforce the point, take a look at this video and see if you can detect any anomalies in the images:

Common persistent EPI artifacts: Receive coil heterogeneity

 
The RF transmit (Tx) and receive (Rx) duties have been performed by separate coils on most commercial clinical scanners for about a decade. These days it's rare to find a combined Tx/Rx coil in-use for brain imaging, although they do exist. (We used one at Berkeley until 2008, on a Varian 4 T scanner.) The separation of Tx and Rx is generally regarded as a good thing because it means a large, body-sized coil can be used for Tx, thereby providing a relatively homogeneous transmission field over a region such as a human head, whereas a smaller (head-sized) coil can be used for Rx, thereby providing the higher intrinsic SNR that comes from using the smallest possible magnetic field detector. (As a general rule the smaller the coil, the higher its SNR close to the coil, because the sensitivity drops off with the reciprocal of distance.)

Indeed, most modern Rx coils aren't single electronic entities at all, but arrays of smaller coil elements put together in a "phased array." The entire phased array acts as a single coil only when the individual signals from individual channels are combined in post-processing. (Each coil element has its own receiver chain - preamplifier and digitizer - allowing separate treatment of signals until after acquisition is complete.) The details of these phased array coils and the combination of the separate signals aren't important at this point, although in subsequent posts they will become important. All we need to focus on right now is simply the fact that a multitude of individually received signals will be combined to produce the final MR signal. (See Note 1.) So, in this post we will consider the receiver characteristics of having multiple discrete coil elements.


Receive fields for phased array coils

Why is the modern Rx head coil a collection of separate circuits? A head-sized, single-circuit Rx coil would detect noise from the entire head, whereas redesigning the coil into a succession of small elements reduces the noise "field of view" for each element. Then, by combining the elements in an appropriate manner, the signal characteristics can be returned (as if a single circuit coil were being used) but with a reduced total noise level in the final images.

It should be relatively obvious that a small wire loop would detect signal with a localized sensitivity profile. The farther away the coil is positioned from the source of an MR signal - from a brain, say - the lower will be the voltage induced in that coil by the available magnetization. We don't need to know the particular mathematics of the receive profile - it's massively complicated for modern Rx coils in any case - so suffice it to say that there's a reciprocal relationship between the signal-to-noise ratio and the proximity of the coil from the magnetization inducing that signal. Closer is better (in SNR terms).

For brain imaging, then, it follows that signal from frontal lobe will primarily be detected by loops at the top of a head RF coil, whereas signal from occipital lobe will primarily be detected by loops at the bottom of the coil. Midbrain regions are where things get most interesting, from an electrical engineering perspective, because we need all the coil's elements combined to get appreciable sensitivity. Thus, we can state another general property of phased array coils: at the spatial scales defined by brain anatomy, a phased array coil offers a heterogeneous receive profile. How heterogeneous? is the important question.

The figure below, taken from Wiggins et al., demonstrates the SNR that can be expected from a typical brain for three different phased arrays. These sensitivity maps don't depict precisely how the Siemens product 12-channel and 32-channel head coils will perform, but we can use this comparison to give us a good idea of what we should be expecting to see in our EPIs because the general properties are consistent: the larger the phased array (i.e. the higher the number of independent elements) the smaller the individual detecting loops, the more heterogeneous the receive profile:

(Click to enlarge.)

Common persistent EPI artifacts: RF interference

 
Time to get back to the artifact recognition series of posts, all of which have the Artifacts label in the footer. RF interference (RFI), or more generally electromagnetic interference (EMI), is another one of the insidious artifacts that can be difficult to diagnose online, during an experiment, unless it becomes catastrophically bad. Your scanner is equipped with sensitive, specific tests for RFI that are used by the service engineer (and probably your physicist) to check for problems, but imaging isn't a sensitive test. Consequently, avoidance rather than diagnosis is usually the preferable option during an fMRI experiment, and a little bit of care and standard operating procedures should suffice to ensure minimal hazards to your data.

I'll begin this post with a description of the nature and sources of RF interference in the MR environment, then provide an example of RF interference in EPI time series data. Next I'll describe the sorts of things you should expect to do when you want to interface a new device, such as a button response box or a physiological monitoring unit, to your scanner as a component of your experiment. It's not - at least, it shouldn't be - a case of "plug n' play!" Finally, I'll describe a simple procedure you can follow to ensure minimal to no problems for your experiment, assuming that your facility has been set up properly.


What is RFI and where does it come from?

A nominal 3 tesla scanner is operating somewhere in the range 120-130 MHz. My scanner is parked at 123 MHz, with a magnetic field strength of 2.89 tesla. (Correct, it's only a 3 T scanner to one significant figure!) A quick glance at the FM dial on an analog radio receiver suggests immediately that the operating frequency of your MRI isn't all that different to your local broadcast radio stations. MRIs aren't the only devices operating at tens and hundreds of MHz in normal operation.

Amazing accounts of fires in and around MRIs

 
An article in the latest installment of The RADIANT is just too remarkable not to share. The article reports two MRI facility fires. In the first, the fire started away from the scanner but ended with the fire out and the magnet still on, surrounded by charred debris. The magnet couldn't be shut down (quenched) because the fire had destroyed the emergency quench circuitry! In the other incident the cause of the fire was the MRI scanner itself; arcing in the gradient cables. Read the article, look at the pictures. Thought-provoking stuff.

THIS MAGNET IS STILL ON!!!! (From http://yfrog.com/nut2nicj)

I'm hyper-sensitive to both of these scenarios, the first because we are about to move my scanner into a brand new building so I am redoing the safety training and reviewing procedures, and the second because my scanner had some serious arcing in 2010. Luckily the arcing was caught before the whole facility went up in flames. Even so... Here's the penetration panel where the gradient power lines enter the magnet room:

 

Note the charring at bottom-right, the negative terminal for the X gradient. That's the gradient used for readout for EPI so it gets by far the most use in my scanner. (FMRI is practically all we do!)

Here's the charred filter removed from the penetration panel:

And here's what ultimately happened at the gradient set, at the other end of the -Gx connection:

This picture was taken as the old gradient set was wheeled away, to be replaced with a new one. The intense heat and vibration had caused the X gradient to short out. Thankfully it was only the gradient and a filter that bought the farm. It could easily have been the entire facility!

 

GRAPPA and multi-band imaging. And motion. Again.

 

It's come to my attention that some of the latest accelerated (aka multiplexed) EPI sequences are now being made available to some sites with vendor/collaborative research agreements, a move that should catalyze their verification, testing and eventual application for neuroscience. The distribution of these pulse sequences to the wider world is great news! The potential is considerable! However, those wanting to conduct neuroscience experiments today with these zippy new tools should bear in mind the not inconsiderable risks. I want to warn you to think very carefully before taking the plunge.

Today's accelerated EPI sequences combine techniques such as multi-band (MB) acquisition with simultaneous echo refocusing (SER) and/or GRAPPA (1,2). In previous posts I've highlighted the increased motion sensitivity of parallel imaging methods such as GRAPPA. The MB family of methods also require "reference scan data" in order to reconstruct the time series images, and as such they are inherently more motion-sensitive than your plain vanilla single-shot EPI. Indeed, similar principles are used to reconstruct MB images as for GRAPPA, and the basic motion sensitivities are the same, i.e. motion during the reference data acquisitions will contaminate all images in a subsequent time series, while motion after the reference data but during the (accelerated) time series will lead to mismatches and spatial artifacts that will degrade temporal stability. In short, using these accelerated sequences is akin to sharpening the motion sensitivity profile of your experiment, and you will need to ensure a high degree of subject compliance to get good data.


Plan, then scan.

Now, I'm not suggesting you dismiss out of hand these sequences for your research. I am suggesting that you apply a lot of forethought, taking the time to consider several important factors. I've written before about evaluating pulse sequences that are new (or new to you). Your first task is to determine whether you even need a fancy, partly validated, highly risky pulse sequence to answer your neuroscience question. If the answer isn't a resounding "yes," why take the risk? Next, you should ask yourself how the pulse sequence should be set up to provide the optimum data. For instance, do you know which slice direction is best for minimizing motion sensitivity and/or receive field bias (g-factor) for the multi-band sequence? And do you know which RF coil to use, and why? If you can't establish your experimental setup based on sound principles that's a suggestion you either don't have the expertise yourself or you aren't collaborating with someone with the requisite expertise. (Me? I could guess, but that's about it! Without doing a validation study of my own I'd be winging it. Which is kinda my point!)

Please don't just go download and use the latest and greatest technique because it's new and cool. I've seen this movie before, and ninety nine times out of a hundred it ends in tears. Please put some justification and logic into your choices before you go and spend hundreds of hours and thousands of dollars finding yet another way that motion can confound an fMRI experiment. Eyes wide open!

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References:

1.  S Moeller, et al. "Multiband multislice GE-EPI at 7 tesla, with 16-fold acceleration using partial parallel imaging with application to high spatial and temporal whole-brain fMRI." Magn. Reson. Med. 63, 1144-53 (2009).

2.  DA Feinberg, et al. "Multiplexed echo planar imaging for sub-second whole brain fMRI and fast diffusion imaging." PLoS ONE 5(12), e15710 (2010).