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!

Sunday, November 27, 2011

Understanding fMRI artifacts: "Good" coronal and sagittal data

Front, back, side to side

Now that you have an appreciation of "good" axial EPI time series data we should be able to zip through a review of "good" coronal and sagittal EPIs. This isn't the post to get deep into the reasons why you might want to acquire these prescriptions instead of axial or axial-oblique slices, but here's a short list (and some music) for you to be going on with:

  • coronal slices tend to exhibit less dropout of frontal and temporal lobes compared to axial slices.
  • coronal slices might permit a smaller field-of-view and higher spatial resolution without signal aliasing than achievable with other prescriptions, assuming your gradient performance and other pulse sequence parameters can be driven sufficiently hard.
  • sagittal slices may also show some improved signal in frontal and temporal lobes compared to axial slices, but the real benefit is the unique coverage afforded. You could acquire a single hemisphere, for instance; could be useful in a handful of situations. Alternatively, if you are interested in the whole brain, including cerebellum and perhaps even brain stem, these structures are naturally included in sagittal slices.
  • sagittal slices tend to make the most common type of head motion - chin to chest rotations - an in-plane phenomenon which might lead to improved motion correction in post-processing.

    There are, naturally, drawbacks to coronal and sagittal slices, just as there are for axial slices. I'll mention some of these in more detail below, as we consider the individual artifacts, but here's another brief list:

    • safety limits on gradient switching (to avoid peripheral nerve stimulation) tend to force the phase encoding direction to be left-right for coronal slices, rendering the EPIs strongly asymmetric. While the absolute level of distortion may actually be very similar to that present in axial slices, the disruption of left-right symmetry can be a shock to your aesthetic sensibility.
    • bizarre distortion is also a "feature" of sagittal slices where, as you'll soon see, the distortion can make the frontal lobes look like a duck's bill! But, as before, the absolute level of distortion may not be significantly different to that in axial slices; it's really the unnatural appearance that shocks us. (We ought to be just as outraged at the symmetric distortions in axial slices!)
    • perhaps the biggest limitation to both coronal and sagittal prescriptions is the number of slices required to cover the entire brain in the given TR. Slicing along the longest axis of the brain, as done for coronal slices, is clearly the least efficient way to do it. The efficiency of sagittal slices falls somewhere between coronal and axial. And, of course, anything that leads to more (fixed width) slices means that TR might have to get longer. It all depends on your application.

      Okay then, that's the introduction over with. Let's now put aside the justification for using one prescription over another and look at what constitutes "good" data in the case of coronal and sagittal slices. The features should be immediately recognizable from what you saw in the axial data of the last post.