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: