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!

Wednesday, September 18, 2013

i-fMRI: BRAIN scanners of the past, present and future

Have you ever wondered why your fMRI scanner is the way it is? Why, for example, is the magnet typically operated at 1.5 or 3 T, and why is there a body-sized transmission coil for the RF? The prosaic answer to these questions is the same: it's what's for sale. We are fortunate that MRI is a cardinal method for radiology, and this clinical utility means that large medical device companies have invested hundreds of millions of dollars (and other currencies) into its development. The hardware and pulse sequences required to do fMRI research aren't fundamentally different from those required to do radiological MRI so we get to use a medical device as a scientific instrument with relative ease.

But what would our fMRI scanners look like today had they been developed as dedicated scientific instruments, with little or no application to something as lucrative as radiology? Surely the scanner-as-research-device would differ in some major ways from that which is equally at home in the hospital or the laboratory. Or would it? While it's clear that the fMRI revolution of the past twenty years has ridden piggyback on the growing clinical importance of diffusion and other advanced anatomical imaging techniques, what's less obvious is the impact of these external factors on how we conduct functional neuroimaging today. State-of-the-art fMRI might have looked quite different had we been forced to develop scanners explicitly for neuroscience.

"I wouldn't start from here, mate."

This week's interim report from the BRAIN Initiative's working group is an opportunity for all of us involved in fMRI to think seriously about our tools. We've come a long way with BOLD contrast to be sure, even though we don't fully understand its origins or its complexities. Should I be delighted or frustrated at my capacity to operate a push-button clinical machine at 3 T in order to get this stuff to work? It's undoubtedly convenient, but at what cost to science?

I can't help but wonder what my fMRI scanner might look like if it was designed specifically for task. Would the polarizing magnet be horizontal or would a subject sit on a chair in a vertical bore? How large would the polarizing magnet be, and what would be its field strength? The gradient set specifications? And finally, if I'm not totally sold on BOLD contrast as my reporting mechanism for neural activity, what sort of signal do I really want? In all cases I am especially interested in why I should prefer one particular answer over the other alternatives.

Note that I'm not suggesting we all dream of voltage-sensitive contrast agents. That's the point of the BRAIN Initiative according to my reading of it. All I'm suggesting is that we spend a few moments considering what we are currently doing, and whether there might be a better way. Unless there has been a remarkable set of coincidences over the last two decades, the chances are good that an fMRI scanner designed specifically for science would have differed in some major ways from the refined medical device that presently occupies my basement lab. There would be more duct tape for a start.


  1. Great post! I would love an upright scanner, I can't help but feel that the prone position causes so much noise and anxiety on the part of the participant.

    1. I think the scanner is too heavy for upright to be feasible. It would be very nice, though.

    2. Yes, this is one issue for sure. To accommodate the same person sitting down, the clear bore of a vertical magnet might have to be wider and shorter than for a horizontal magnet. That would tend to limit the maximum field strength of a vertical bore magnet, but there is probably no technical reason - only financial ones - why a vertical bore "head-only" 3 T scanner couldn't be built.

      Just for the sake of completeness, if the vertical bore magnet could be built even larger, such that the polarizing field direction were anterior-posterior rather than head-to-foot, then there would be a minor benefit of slightly improved magnetic susceptibility gradients across the brain. I forget the reference, but a few years ago someone showed in a conference poster that having the magnetic field A-P reduces slightly the cruddy gradients from sinuses. But if the magnet is a solenoid the clear bore gets very big indeed to accommodate even a seated subject! (Imagine trying to sit in a chair in the middle of a normal, horizontal bore magnet. It would have to be x2 to x3 larger i.d.!)

  2. Both subjects and IRBs are huge fans of duct tape.

    1. I'm a fan of Velcro, myself. Makes me feel more NASA than Home Improvement!