Thursday, April 21, 2011

Tactical approaches to (re)shimming

In an earlier post I looked at the effects of heating on the temporal stability of EPI data. Particular attention was given to the translations in the phase encoding dimension that arise whenever the scanner drifts off resonance during imaging, through the heating and subsequent cooling of the gradient coil (rapid time constants) as well as of the passive iron shims between the gradient coil and the magnet cryostat (slow time constants). These frequency shifts are most apparent between blocks of EPI as discontinuities, or steps, in a concatenated time series, because of the on-resonance adjustment that precedes the start of each EPI block.

Fortunately, for a typical modern scanner there is little detrimental effect on the temporal SNR (and statistical power) of the total time series once it has been corrected for motion using a standard rigid-body realignment algorithm. But the outstanding question is this: must we rely so heavily on the realignment algorithm to fix what is really a hardware limitation? Surely, fixing it in software is a hack? (Save the jokes, I've almost certainly heard them! See Note 1, below.) And, as pointed out by El-Sharkawy et al., if the magnetic field is being perturbed sufficiently by heating to cause components with a Z spatial dependence to change, what about all the other spatial dependencies? If the shim is being compromised, why not do something about it?

The standard fMRI protocol

Let's start by reviewing what happens in a standard protocol. On Siemens scanners, at least, the usual approach to an fMRI experiment is to shim at the start of the session and then not re-shim unless there is a substantial change in the prescribed imaging volume (the stack of EPI slices). Shimming is initiated by the first scan that's not a localizer. (See Note 2.) So, if a 3D anatomical, such as an MP-RAGE, is acquired after the localizer and before the first EPI, say, there will be no further shimming during the session (unless requested by the operator).

Assessing the problem

Now, we could continue to investigate shimming as a means to mitigate the effects of heating using experiments on phantoms. That would be a full study in and of itself. To keep this post shorter and more relevant to you, I'm going to jump straight to brain data. That's because when we are talking about shimming (or re-shimming), we are going to mix the effects of scanner heating with our old chum, subject movement. We're going to lump everything together and look at the resultant. Put another way, there's no point in coming up with a putative solution to the heating issue if it could exacerbate the movement issue.

Experimental verification

Very briefly, as part of a vision experiment, shimming was performed (or not) between blocks of 150 volumes of EPI, TR=2 seconds. (Siemens users: See Note 3.) During the first session, shimming was performed between blocks for the first five blocks, then shimming was omitted between blocks for the next five. The time gaps between blocks weren't controlled rigorously; it was whatever was required to set up a new stimulus script plus, when appropriate, the 30-odd seconds to re-shim. A typical inter-block gap was between one and two minutes. In a second session on the same subject the ordering was reversed: shimming was omitted for the first five blocks, then performed between blocks for the final five blocks.