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.


Preliminaries

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.

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.

Siemens slice ordering

I've heard on the wind that there is still confusion or even a total lack of awareness of the change in slice ordering for interleaved slices when going from an odd number to an even number of slices, or vice versa. It makes a big difference for slice timing correction. So I though I'd post below a section from my user training guide/FAQ as a ready reference. Note that as far as I know this change in slice ordering is only an issue for Siemens scanners running VB15 or VB17 software, I can't comment on VD11 or other versions, and I haven't actually tested any scanner platform except a TIM Trio. Furthermore, it's only an issue if you're using interleaved slices. If anyone has additional information, especially if it conflicts with the situation posted here, then the field would probably appreciate a comment!

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In what order does the scanner acquire EPI slices?

There are three options for slice ordering for EPI. To understand the ordering you first need to know the Siemens reference frame for the slice axis: the negative direction is [Right, Anterior, Foot] and the positive direction is [Left, Posterior, Head]. The modes are then:

• Ascending - In this mode, slices are acquired from the negative direction to the positive direction.
• Descending - In this mode, slices are acquired from the positive direction to the negative direction.
• Interleaved - In this mode, the order of acquisition depends on the number of slices acquired:
• If there is an odd number of slices, say 27, the slices will be collected as:

1 3 5 7 9 11 13 15 17 19 21 23 25 27 2 4 6 8 10 12 14 16 18 20 22 24 26.

• If there is an even number of slices (say 28) the slices will be collected as:

2 4 6 8 10 12 14 16 18 20 22 24 26 28 1 3 5 7 9 11 13 15 17 19 21 23 25 27.

Interleaved always goes in the negative to positive direction, e.g. foot-to-head for transverse slices.

So, if you are doing 28 interleaved axial slices the order will be evens then odds in the foot-to-head direction. 27 interleaved axial slices would also be acquired in the foot-to-head direction but would be in the order odds then evens. If you switch to 28 descending axial slices the acquisition order will become 1,2,3,4,5…28 and the direction will swap to being head-to-foot.

Physics for understanding fMRI artifacts: Part Thirteen

A tour through a real EPI pulse sequence

In some posts I've got planned it will be important for you to know something about all of the different functional modules that are included in a real EPI pulse sequence. So far in this PFUFA series I've used schematics of the particular segment of the sequence that I was writing about, e.g. the echo train that covers 2D k-space for single-shot EPI. Except that there comes a time when you need to know about the sequence in its entirety, as it is implemented on a scanner. Why? Because there are various events that I've given short shrift - fat saturation and N/2 ghost correction, for instance - that have significant temporal overheads in the sequence, and these additional delays obviously affect how quickly one can scan a brain.

So, without further ado, here is a pulse sequence for fat-suppressed, single-shot gradient echo EPI, as used for fMRI:

(Click to enlarge.)

Okay, so it's not the entire pulse sequence. The readout gradient echo train in this diagram has been curtailed after just nine of 64 total gradient echoes that will be acquired, for EPI with a matrix of 64x64 pixels. The omitted 55 echoes are simply clones of the nine echoes that you can see. (Note that there are no additional gradient episodes at the end of this particular EPI sequence; all the crusher gradients occur at the start of the sequence and these are visible in the above figure. More on crusher gradients below.) I should also point out that this is the timing diagram for acquisition of a single 64x64 matrix EPI slice. The pulse sequence as shown would be repeated n times for n slices within each TR. (See Note 1.)


Interpreting what you see

Let's first determine what information is being displayed on the figure above. There are five axes, all handily labeled on the far right-hand side of the figure. The top axis is the RF transmit channel; we've got two RF pulses in this sequence. The second axis down is the receiver, or analog-to-digital converter (ADC) channel. The scanner is receiving signals only when there's a rectangle specified on the second axis. Finally, the bottom three axes represent the pulsed field gradients, in the order X, Y, Z.

Just for fun, let's quickly determine what the scanner is doing in the logical frame of reference, before we delve into the nitty-gritty. The slice selection gradient will occur in concert with an RF excitation pulse, and we have two RF pulses to choose from. Slice selection can't be the first RF pulse because that pulse occurs without any concomitant gradients. Thus, the slice excitation pulse must be the second one and we can deduce that slice selection is along the Z axis, which is the magnet bore axis. We're doing axial slices.