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!

Thursday, October 13, 2016

Motion traces for the respiratory oscillations in EPI and SMS-EPI

This is a follow-up post to Respiratory oscillations in EPI and SMS-EPI. Thanks to Jo Etzel at WashU, you may view here the apparent head motion reported by the realignment algorithm in SPM12 for the experiments described in the previous post. Each time series is 200 volumes long, TR=1000 ms per volume. The realignment algorithm uses the first volume in each series as the template. The motion is plotted in the laboratory frame, where Z is the magnet bore axis (head-to-foot for a supine subject), X is left-right and Y is anterior-posterior for a supine subject.

In the last post I said that there were five total episodes of a deep breath followed by sigh-like exhale, but actually the subject produced a breath-exhale on average every 30 seconds throughout the runs. (This was a self-paced exercise.) Thus, what you see below (and in the prior post) has a rather large degree of behavioral variability. Still, the main points I made previously are confirmed in the motion traces. I'll begin with the axial scan comparison. Here are the motion parameters for the MB=6 axial acquisition with standard foam head restraint (left) versus the custom printed restraint (right):

MB=6, axial slices. Left: foam restraint. Right: custom 3D printed headcase restraint

The effect of the custom restraint is quite clear. The deep breath-then-sigh episodes are especially apparent when using only foam restraint. Note the rather similar appearance of the high frequency oscillations, particularly apparent in the blue (Y axis) traces between the two restraint systems, suggesting that the origin of these fluctuations is B0 modulation from chest motion rather than direct mechanical motion of the head. We cannot yet be sure of this explanation, however, and I am keeping an open mind just in case there are small movements that the custom head restraint doesn't fix.

Friday, October 7, 2016

Respiratory oscillations in EPI and SMS-EPI

tl;dr   When using SMS there is a tendency to acquire smaller voxels as well as use shorter TR. There are three mechanisms contributing to the visibility of respiratory motion with SMS-EPI compared to conventional EPI. Firstly, smaller voxels exhibit higher apparent motion sensitivity than larger voxels. What was intra-voxel motion becomes inter-voxel motion, and you see/detect it. Secondly, higher in-plane resolution means greater distortion via the extended EPI readout echo train, and therefore greater sensitivity to changes in B0. Finally, shorter TR tends to enhance the fine structure in motion parameters, often revealing oscillations that were smoothed at longer TR. Hence, it's not the SMS method itself but the voxel dimensions, in-plane EPI parameters and TR that are driving the apparent sensitivity to respiration. Similar respiration sensitivity is obtained with conventional single-shot EPI as for SMS-EPI when spatial and temporal parameters are matched.


The effects of chest motion on the main magnetic field, B0, are well-known. Even so, I was somewhat surprised when I began receiving reports of likely respiratory oscillations in simultaneous multi-slice (SMS) EPI data acquired across a number of projects, centers and scanner manufacturers. (See Note 1.) Was it simply a case of a new method getting extra attention, revealing an issue that had been present but largely overlooked in regular EPI scans? Or was the SMS scheme exhibiting a new, or exacerbated, problem?

Upper section of Fig. 4 from Power,, showing the relationship between apparent head motion (red trace) reported from a realignment algorithm and chest motion (blue trace) recorded by a respiratory belt. See the paper for an explanation of the bottom B&W panel.

Wednesday, June 29, 2016

Starting points for SMS-EPI at 3 T: Part II

In an earlier post I presented three starting protocols for the CMRR version of SMS-EPI, referred to as the MB-EPI sequence here. I'll use italics to indicate a specific pulse sequence whereas SMS-EPI, no italics, refers to the family of simultaneous multi-slice methods. In this post I'll develop a similar set of three starting protocols for the Massachusetts General Hospital (MGH) version of SMS-EPI, called Blipped-CAIPI. I'm going to build upon the explanations of the last post so please cross reference for parameter explanations and background.

As for the previous post there are several things to bear in mind. This series is Siemens-centric, specifically Trio-centric. While many of the concepts and parameter options may apply to other platforms there will be minor differences in parameter naming conventions and, perhaps, major differences in implementation that you will need to consider before you proceed. For Siemens users, I am running aging software, syngoMR version B17A. The age of the software and the old reconstruction board on the scanner means that you can expect to see much faster reconstruction on a newer system. I hope, but cannot guarantee, that the actual image quality and artifact level won't differ massively from a Trio running VB17A to a new Prisma running VE11C. I'll keep you updated as I learn more.


As before, for this post I am going to be using a 32-channel receive-only head coil. The SMS-EPI sequences can be made to work with a 12-channel coil but only in a reduced fashion because the 12-channel coil has minimal receive field heterogeneity along the magnet z axis - the struts run parallel with the magnet axis except at the coil's rear, where they converge - and generally we want to do axial slices (along z) for fMRI. I don't yet know whether SMS-EPI would work well on the 20-channel head/neck coil on a Prisma, it's something I hope to investigate in the near future. But a 64-channel head/neck coil on a Prisma will definitely work for SMS-EPI. Better or worse than a 32-channel coil on a Prisma? I have no idea yet.

The Blipped-CAIPI sequence version 2.2 was obtained through a C2P (Core Competence Partnership) with MGH. Installation was a breeze: a single executable to port to the scanner and one click, done. The development team offers an informative but brief 7-page manual which will be useful to anyone who has read the SMS-EPI literature and has a basic understanding of how SMS works. It's not a starting point for everyday neuroscience, however. The manual mentions a .edx (protocol) file as a starting point for 2, 2.5 and 3 mm resolution scans, but in the file I downloaded for VB17A the contents didn't include it. Perhaps contact MGH if you are on another software version and you'd like a .edx file rather than building your own protocol, e.g. by recreating what you see here.

Tuesday, June 28, 2016

Exploiting Tanzania

So a massive helium reserve may have been found in Tanzania's Rift Valley. Wonderful. All the western headlines this morning have put a typically western spin on it. Hurrah! We are saved! We get to go plunder a foreign place again for what we need to save our own lives! Before we get too carried away with ourselves, let's take a few seconds to think about a few things. Like, say, how many MRI scanners are there in Tanzania right now? How many Tanzanian lives will be saved? Anyone care to estimate? This scanner in Dar es Salaam makes headlines when it breaks down.

What about the wildlife in Tanzania? Will lives be saved there, too? Note the concentration of national parks and game reserves in and around the Rukwa region of Tanzania. Now, I'm not intimately familiar with how helium gas is extracted, concentrated or liquefied but I'm going to guess that some of it has to be done where the gas is found. Even if the gas doesn't just float conveniently into collection chambers instead of needing some sort of gas forcing process (We love fracking, right?) and miles and miles of pipelines, it's a fair assumption that there will be massive energy needs to liquefy it. Then the cryogenic liquid helium must be transported. So we'll need roads, maybe an airport for the suits to get in and out quickly, and perhaps a railway to move the product to a sea port. Or we could just push the gas down a long pipe to the coast where it could be liquefied, then transported abroad. This is all going to be great news for African nature, I'm sure of it!

Tuesday, February 9, 2016

Starting points for SMS-EPI at 3 T

Several people have approached me for advice on using simultaneous multi-slice (SMS) EPI for fMRI experiments. This is the sequence also known as multiband (MB) EPI. I'll come back to nomenclature in a moment. First, though, a brief introduction to what may become a lengthy series of posts. I'm going to focus on BOLD-based fMRI exclusively for the time being - sorry diffusion and ASL folks - and because I presently only have a Siemens Trio at my disposal, everything I write will have strong bias in that direction. That said, I do anticipate writing later posts dealing with SMS-EPI (for fMRI) on a Siemens Prisma at least, and I can already envisage a need for posts dealing with receive field normalization, in-plane parallel imaging, distortion correction options, reconstruction options and multi-echo SMS, to name just a few advanced topics. But first things first - to get going!

Options for SMS-EPI on a Siemens 3 T scanner

I am aware of three SMS-EPI pulse sequences for a Siemens Trio. One comes from the University of Minnesota's Center for Magnetic Resonance Research (hereafter CMRR), one comes from the Martinos Center for Biomedical Imaging at Massachusetts General Hospital (hereafter MGH), and one comes from Siemens as a work-in-progress (WIP) aftermarket sequence. For this post I'm going to be using the sequence provided by CMRR. Since CMRR refer to their sequence as multiband (MB) EPI I shall stick to this nomenclature here, and reserve the term SMS-EPI to apply to the broader family of pulse sequences. I may do posts on the MGH and WIP sequences in the future, but the CMRR sequence has been used the most broadly to date (e.g. the Human Connectome Project, which I'll discuss at length below) and so it offers the most immediate, road-tested place to start.

Friday, February 5, 2016

Corrective lenses for tight head coils

Most labs have plastic goggles for correcting a subject's vision in the MRI. Here's our box of tricks:

These goggles work pretty well for a standard sized head coil, such as the 12-channel TIM coil on my Siemens Trio. But for a tighter fitting coil, such as the 32-channel head coil, there is simply no way to cram a subject wearing goggles into the space available. For a start the goggles' frame prevents the subject's nose from penetrating the appropriate gap in the front of the coil.

A simple solution is to relocate the corrective lenses on the outer surface of the head coil. All that's required is a different way to hold the lenses in place. My ace engineer, Rick, made this pair of holders for our 32-channel coil:

Wednesday, December 2, 2015

Making tracks for charity

This is going to be among the more unusual blog posts I've written. Here goes nothing.

The back story. A few years ago I decided to take a stab at writing fiction. The result was Bubble Chamber, an academic satire with a scientific twist. My intention? To see if I could write a novel, to actually finish it and get it into the public domain as an end point. Check! The process wasn't even sufficiently painful to dissuade me from future forays into novel writing. Just not yet, I have too many other irons in the old fire.

Towards the bottom of the post you can read a synopsis of Bubble Chamber along with a little contrived biography of yours truly. I am also tempted to include here a link to Amazon so that you might procure a copy of my literary scribbling for yourself. But I won't do that just yet. We need to make a quick detour.

Dementia Adventure

It transpires that a young Englishman by the name of Chris Graham has been steadily riding his bicycle, solo and unsupported, around the circumference of Canada and the USA since the beginning of May. He is now in Maine, approaching Canada for the second time and about to commence the last leg of his marathon journey. His current location, as well as the route already completed, can be seen in real time courtesy of his YBTracking page. A flight back home to the UK on Christmas Eve beckons as the final reward for all of Chris's hard work. (Motto: If in doubt, pedal!)

Chris is doing his ride for charity. Specifically, Chris is raising money for Alzheimer's Research UK. You see, Chris is likely to develop dementia in a not too distant future. He carries the gene for early onset Alzheimer's, a disease that has claimed the lives of many of his close relatives, including is father and grandfather, at an age that Chris himself is now rapidly approaching. You can learn more about Chris and his family history on his web page.

This is no sob story, however. Far from it. In fact, following Chris on his Facebook page has brought smiles and laughs to many thousands of people this year. Watch one of his video updates then tell me you won't be back to see what happens next! Better yet, quit reading this blog and pop on over to Chris's Just Giving web page to send him some money right now, then go peruse the photos and videos on his Facebook page. Thanks, and goodbye!

If I didn't just lose you to an immediate donation then I have a proposition for you. Chris is a mere three lousy UK grand from hitting a £40K target and I want to do a little something to help him get there. All proceeds arising out of sales of my aforementioned novel were committed 100% to charity from the moment I conceived of writing it. That hasn't and won't change. An assisted living charity in the eastern US has received very occasional, very small checks over the years. But for the rest of this year at least, all proceeds from sales of Bubble Chamber - available via this Amazon page - will go to Dementia Adventure. I am also going to send along an equivalent amount of my own money for each copy sold so that you have extra inducement to go buy the book.

If you prefer to ignore my book entirely and simply donate to Chris that is just peachy. Or donate to Chris and then go buy the book, I won't stop you. Either way, join Chris virtually as he goes into the last three weeks of a truly epic bike ride. Along the way, take the time to think about just what it is you want to achieve with what remains of your life. We could probably all use a little bit more of Chris Graham's irrepressible spirit.