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 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.

Saturday, October 3, 2015

Functional MRI of dolphins?


Those of you who follow me on Twitter may have noticed that I've been scanning some post mortem brains of Cetacea over the past year or so. That's whales, dolphins and porpoises to you and me. The brains come in all shapes and sizes, from a rather tiny Amazon river dolphin, about the size of a fist, to fin and sei whale brains that are so wide they have to be inserted sideways, hemisphere-first, into the 3 T (human) head coil. The conditions and ages of the brains vary tremendously as well. Some have been fixed in formaldehyde for decades yet yield remarkably decent signal, others have been stored in ethanol and are as hard as rubber with T2 to match. A few months ago we obtained a recently deceased fresh brain of a white-sided dolphin which we were able to scan within about twelve hours of its demise. The image quality was magnificent.

What do we plan to do with all the post mortem data? That is still being formulated. Initial motivation for the project came from some Berkeley anthropologists with an interest in comparative neuroanatomy across higher mammalian species. Coincidentally, Greg Berns' group at Emory has recently produced a nice example of dolphin brain tractography and his recent study is a good example of what might be done in future. There's a commentary on Greg's study here, and an example image from his paper below. We are now determining how we might combine resources, share data and all that good stuff. More on what will be available to whom and when as we progress.

From: Berns et al.

In any case, after I posted the white-sided dolphin MRI to Twitter someone asked, likely facetiously (I suppose that should be flippantly), whether functional MRI was next. FMRI of dolphins was the subject of an April Fool's Day joke a few years ago, and it does seem far-fetched at first blush. So, too, does studying trained dogs with fMRI, but Greg Berns' team is already doing that. Since thought experiments are cheap I figured I'd write a blog post to consider what might be feasible today if one were sufficiently motivated (read sufficiently well funded) to want to do fMRI of cetaceans. If nothing else we might learn something as we're forced to consider the manifold factors.

Thursday, July 9, 2015

Functional MRI of trained dogs


One of the delightful aspects of running an imaging facility is the sheer variety of projects coming through the door. Late last year my boss told me he'd been discussing with a group from Emory University about doing fMRI on trained dogs at our center. I'll confess to receiving the suggestion unenthusiastically, if only because I envisioned a mass of bureaucracy followed by a head-on logistical collision between the dog group and the dozens of human users. Activity at our center oscillates between hectic and frenetic, depending on the day. But, as it turned out I needn't have worried. The bureaucracy was handled admirably by the Emory folks while the logistical issues simply failed to materialize because of the professionalism of the dog fMRI team. It's been an enjoyable experience. And there are dogs. Many boisterous, happy, playful yet exceedingly well-trained dogs. Like these:


Monday, May 18, 2015

Checklist for fMRI acquisition methods reporting in the literature: version 1.3


The latest version of the fMRI acquisition checklist is now available at The Winnower via this link. It can also be located/cited using DOI: 10.15200/winn.143191.17127 .

Updates/changes from v1.2:
  • The “Pre-scan normalization” parameter has been renamed “Signal intensity correction/normalization” to broaden its scope.
  • Reviewed and revised explanatory notes.
  • New parameters: RO partial Fourier scheme, Number of echoes, Saturation bands, Gradient non-linearity correction, Z-shim gradient correction, On-resonance adjustment.

The current list should work now for most simultaneous multislice (SMS) EPI, multi-echo EPI (or spiral) and 7 T experiments, but additional emphasis will be placed on these advanced methods in the next round. Please let me know of parameters you'd like included. The next planned update will include as far as possible the vendor-specific nomenclature for each parameter. I anticipate a late 2015 release date. There are no plans yet to do a machine-readable version of the checklist, as originally discussed, but that is only because nobody has been asking for it. Please get in touch if this is something you're interested in.


Thursday, May 14, 2015

Uploading to The Winnower from Blogger: A real time tutorial


So I have a memory like a sieve except that it's profoundly less useful in the kitchen. And because I know from painful experience that anything I don't document never happened, I am going to help myself and you by creating in real time a tutorial to upload blog posts from Blogger to The Winnower, should you be so inclined. Why do it? DOI is one reason.

Those of you who were smart enough to begin your blog's existence on Wordpress can use a fancy plugin for your API. Those of us who now have too much inertia on Blogger to relocate must do a little more work and use some intermediate steps, but it really isn't that hard. What's more, the intermediate steps offer an opportunity for proofreading and fine-tuning that you might like to do anyway. Let's do it!