Increasing the acquisition angle up about 20-30 degrees from axial can improve the overall signal drop-out problems due to the way the susceptibility gradients typically manifest. See, e.g.:
Neuroimage. 2003 Jun;19(2 Pt 1):430-41. Related Articles, Optimized EPI for fMRI studies of the orbitofrontal cortex.
Best,
VDC
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf
> Of Dave Langers
> Sent: Tuesday, August 26, 2014 10:34 AM
> To: [log in to unmask]
> Subject: Re: [SPM] Theoretical questions on fMRI acquisition and analyses
>
> > 1) I see some papers reporting the angle at which axial images are acquired. Why is this
> angle non-zero?
> > 2) Why is the plane (orientation) in which images are acquired such an important
> parameter of an MRI scan
>
> Perhaps you are referring to the flip angle? The angle of the volume orientation is another
> angle, but I've seldomly seen it reported as a number (usually just a description, like slice
> were approximately aligned to this-or-that brain structure). The flip angle refers to the spin
> physics and plays a major role in the contrast of the image. This one must be non-zero for
> an RF-excitation to have any effect.
> If you do mean orientation angle, then it doesn't seem overly important indeed. Unless you
> have non-isotropic resolution (different in-plne resolution from slice thickness), in which
> case it may be useful to know in which direction data are how accurate. Also, when judging
> artifacts (from scanner, or from interpolation), the orientation is relevant of course.
>
> > 3) What is the safest thing to assume when papers report coordinates but do not specify A.
> whether they are in voxels or in mm B. whether they represent the coordinates of the centre-
> of-gravity (i.e. the stats-weighted mean) or those of the maximum (peak) activation?
>
> Coordinates are virtually always in MNI space if these are normalised data (sometimes
> Talairach, which is comparable but not identical). This corresponds with voxels or mm if
> you have a 1mm resolution normalised template, but better just see it as dimensionless
> numbers in a standard coordinate space. Whether it concerns peaks or centre-of-mass
> should hopefully follow from the paper; if nothing is said, most likely it will be a peak
> coordinate (the largest peak in the connected blob, if there is only one reported).
>
> > 4) Why is it that some papers quantify BOLD signal strength (activation) as a t-stat
> whereas others report a z-stat?
>
> It is always a measure of significance, that is the ratio of effect size, i.e. fMRI response
> amplitude, relative to the standard error of the same. The t-value really is like a z-value,
> except that it accounts for the fact that the effect size and standard error were determined
> from the same (small) sample, in which case the shape of the distribution changes slightly.
> You can convert t-values to p-values, and those to z-values if you like. Conceptually, t and z
> is quite comparable, and for large numbers of degrees of freedom, even the numbers are
> alike. I don't have any idea why some people feel a need to convert to z if the original result
> was t.
>
> And then your most interesting question, if you ask me: ;)
> > 5) Why is activation strength quantified in terms of significance (it seems most heatmaps
> are based on p- or t-values) and not on some measure of effect size, which seems to me
> would better justify the term "strength of activation"?
>
> I agree! Both are different ways of stating something about "strength". The betas
> themselves, preferably normalised to the baseline level and expressed as a percentage signal
> change, quantify the magnitude of the effect in the brain. It does depend on the imaging
> sequence, so it still isn't intrinsically "meaningful" as a biological measure, but it allows you
> to compare more easily across studies with similar paradigms. The t/p/F-value says someting
> about the significance of the effect, so how confident you can be the effect is real (or much
> better: how unlikely the observation is if the effect were zero!). Significance depends on
> sample size, effect size doesn't. Sometimes one is more interesting (when trying to reject
> some theory as not fitting with the data, for instance) and sometimes the other is more
> interesting (when trying to get some idea how physiologically/clinically relevant an effect
> seems to be, for instance). Ideally, report on both; effect sizes are reported far too little, if
> you ask me.
>
> Dave