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, July 3, 2012

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.