Dear Chris, Dave and Vince, thank you so much for helping out with my questions! Just to clarify on the first two, I was indeed referring to the viewing angle not from an MR-physics sense but simply from a viewer sense, so for instance I'd have assumed that when looking at an axial image like this:

..that this is what you "see" when looking at the brain from directly underneath (or above, I suppose, depending on whether a radiological or neurological convention is used) , i.e. perpendicular to the body's vertical axis.

I am still not sure whether this is indeed the case, or whether the non-zero angle of acquisition (assuming, say, an axial plane orientation) means that this viewing angle is also non-zero, i.e. the axial plane corresponding to the view is not perfectly horizontal but a horizontal plane tilted a number of degrees along any combination of the remaining 2 axes.

Chris, you mention you've seen axial scans containing both AC and PC, but surely these landmarks are already in the same horizontal plane, no?

Also, is it correct, then, to say that when going through e.g. coronal slices of an MRI scan, these will look roughly the same regardless of whether the acquisition orientation was saggital or axial, but that the distortions will be slightly different?

Thanks again!

--Francesco

On 26 August 2014 18:45, Vince Calhoun <[log in to unmask]> wrote:

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