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, 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!