Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Tuesday, February 28, 2012

Common persistent EPI artifacts: Distortion and dropout

The origins of distortion and dropout in EPI were covered in PFUFA Part Twelve, and both of these artifacts have been mentioned in passing in the previous articles concerning abnormally high ghosting. In some instances these artifacts are "co-morbid" because certain issues that cause abnormally high ghosting - such as a poor shim because of asymmetric placement of the subject's head in the magnet - are likely to increase distortion and dropout effects at the same time. Except that it can be very difficult to evaluate distortion and dropout by inspection, during an experiment. The ghosts can be used as a fairly independent "barometer" of the experiment's quality if, as is often the case, some of them fall into an image region that is otherwise noise. Not so with distortion and dropout. By definition these artifacts plague signal regions in the brain, and even an experienced operator can have a tough time determining when either issue is worse than it might otherwise be.

So I'm afraid I don't have a whole lot of new information to offer on either distortion or dropout, from the perspective of diagnosing and potentially changing (improving) your experiment on the day. Other than very obvious deficiencies, as might happen if the subject has a highly conductive hair product, for example, I don't spend much time evaluating distortion or dropout by inspection. Ghosts can be a good surrogate for all that ails distortion and dropout, so I focus on those.

Where you can potentially improve the situation for distortion and dropout is with parameter selection when you are establishing your experimental protocol. Distortion and dropout will generally change with slice prescription, as we already saw in the "good data" posts. And it may be that reduction of dropout leads you to use a particular slice direction, e.g. coronal slices for improved frontal lobe signal. After that, the other common tactics to minimize dropout are to use the thinnest possible slice thickness, possibly using higher in-plane spatial resolution, and perhaps decrease TE. These are protocol/parameter questions that are covered somewhat in my user training guide/FAQ, and I will expand on those sections below. Be warned, however, that it is very difficult to provide general guidelines for all fMRI experiments. Instead, the parameter choices tend to be dictated by your primary requirements. You might select very different parameters for a study that is primarily interested in orbitofrontal cortex than you would use for a sensorimotor task. It's horses for courses.

Approaches to tackling distortion

The level of distortion in the phase encoding dimension is a function of the echo spacing, as explained in PFUFA Part Twelve. Tactics to reduce the distortion level involve making fundamental changes to the phase encoding k-space scheme, e.g. multi-shot segmented k-space, or parallel imaging methods. In each approach the essential idea is to increase the k-space step size, thereby increasing the bandwidth of the phase encoding dimension.

Sunday, February 19, 2012

Terminology change: characterizing EPI artifacts

After considering the rest of the topics that I want to cover in the series of posts on EPI artifacts, I've decided to change the terms "static" and "dynamic" to "persistent" and "intermittent," respectively. I think the new terms better reflect the dominant temporal character of each artifact. The idea is to sort them based on whether they are likely to plague every frame of an EPI time series, or come and go.

Take external RF interference, for example. Say you fail to close properly the RF-sealed door to the magnet room and the door opens slightly during your scan, leading to RF contamination from "environmental" sources. In this instance the RF interference itself isn't likely to be static - it will vary with whatever sources of RF happen to be in your scanner environment - but it will persist (at some level) until the door is closed. With a good eye or some appropriate diagnostics it would be possible to show the persistence of the problem throughout an acquisition. Contrast this situation with a static electrical discharge somewhere within the scanner room; tiny sparks that cause a broad range of electromagnetic frequencies, including radiofrequencies. These can arise if the humidity of the magnet room air becomes too low. Depending on the source of the sparks, the humidity, etc. you might find that only one or two TRs of a time series are contaminated, or you could find the entire time series is affected. I will therefore characterize static electrical discharges as an intermittent artifact.

Pedants will spot that the first example can be modulated by the position of the magnet room door, rendering the artifact intermittent, while in the second example the propensity for static electrical discharges will persist as long as the source exists, while the humidity remains low, etc. So, yeah, in some ways the distinctions I'm making are subjective. FMRI, like life, is complicated! Still, I'm hopeful that a more practical characterization of artifacts will assist you in differentiating and diagnosing them when it matters: during your experiment. And once you're an expert you will find it easy to comprehend the nuances of temporal behavior, when my artificial distinctions will be all but irrelevant to you.

So, there you have it. I'll be going back to edit the existing posts in this series over the next couple of days. Apologies for any confusion the switch creates.

Thursday, February 16, 2012

Physics for understanding fMRI artifacts: CONTENTS

Figured it might be useful to have some summary/contents pages. I'll do similar admin posts as the other series mature, too. And I will label these pages with "Contents" to make them easier to find via the sidebar.

Part One

An introduction to the series, followed by an introductory video courtesy of Sir Paul Callaghan: What is NMR and how does it work?

Part Two

Further videos explaining the principles of nuclear magnetic resonance - how the intrinsic spin of certain atomic nuclei interacts with applied magnetic fields to yield useful information.

Part Three

Videos showing the anatomy of a miniature scanner, a basic NMR experiment, why shimming is important for NMR (and MRI), how and why a spin echo works, and the relaxation of spins back towards their ground state.

Part Four

Mathematics of oscillations: an introduction to imaginary and complex numbers, and frequency and phase.

Wednesday, February 15, 2012

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

In the previous post I covered sources of persistent ghosts that arise as a result of some property of the subject, such as the orientation of the subject's head in the magnet. These are what I'm categorizing as subject-dependent effects. In this post I will review the most common sources of persistent ghosts attributable to the scanner, either from an intrinsic property that you might encounter inadvertently, or from mis-setting a parameter in your protocol. As I mentioned last time, I am restricting the discussion to factors that you have some control over as the scanner operator. Ghosts that arise because of a scanner installation error, such as poor gradient eddy current compensation or inaccurate gradient calibration, are issues for your facility physicist and/or your service engineer.

Scanner-dependent conditions:

Rotated read/phase encode axes 

GLOBAL - affects all slices to some extent.

This is an insidious problem that we could categorize as pilot error, except that it's very easily encountered without realizing it. When you set up your slice prescription you are primarily concerned with capturing all those brain regions you need for your experiment. Or you might be concerned with setting a particular slice angle relative to the brain anatomy, e.g. parallel to AC-PC. Now, if the subject's head is precisely aligned such that the read and phase encode axes of your imaging plane are matched perfectly with the gradient set axes (i.e. with the magnet's frame of reference), then for axial slices the readout dimension will be attained using pure X gradient (subject's left-right) while the phase encode dimension uses pure Y gradient (subject's anterior-posterior). (See Note 4 in the post on "Good" coronal and sagittal data for an explanation of why the gradients are established this way, for subject safety/comfort reasons.) But, if the head is twisted slightly, or you're a little sloppy with your slice positioning, then it is quite easy to have a readout gradient that is mostly X with a little bit of Y, and a phase encoding gradient that is mostly Y with a little bit of X. This in-plane rotation ought not be a problem if the X and Y gradients performed equivalently, but they're only similar and not identical. There tend to be small differences in the response time of the gradients, which means that when the scanner tries to drive the read gradient to its desired k-space trajectory, one component (say the X component) can respond faster than the other. This produces a slight mismatch between the target (ideal) k-space trajectory and the trajectory that's actually achieved by the gradients, thereby leading to a source of zigzags that will produce N/2 ghosting.

Now the good news. You've got to rotate the image plane by quite a lot before the ghosting starts to become apparent. It's common to have rotations of 1-2 degrees and these will generate almost no additional ghosting. Once the rotation gets much larger than 5 degrees (depending on the specifics of your scanner) then you might start to see additional ghosting. Below on the left is an ideal prescription, while on the right I've intentionally rotated the image plane by 8 degrees, leading to a small but noticeable increase in ghost level:

(Click to enlarge.)