Ah yes, another case of SIFT2-derived connection density estimates having the opposite direction of effect to that expected… I seem to be collecting these! Maybe I accidentally left a negative sign somewhere in the code…
tcksift2 doesn’t have a
-term_mu option; indeed the value of mu does not change at all within the SIFT2 algorithm.
tcksift has a
-term_mu option (the original intent of which was actually to obviate the need for explicit multiplication by mu); but if you’re using that, you’d need more than 500k streamlines, and you wouldn’t be dealing with weights. Maybe you meant
Just to mention that after refining pathways, the streamline counts do not remain identical among subjects.
This would also be the case without refining pathways: the number of streamlines within the original whole-brain tractogram that are appropriately ascribed to the pathway of interest and hence also contribute to that count would also vary between subjects.
I assume that FBC should not be influenced by the number of streamlines, but it also doesn’t biologically make sense that someone with less brain volume is getting more fiber density because of having more streamlines.
It’s not quite correct to say that FBC is elevated “because of having more streamlines”, since that excludes the possibility of differential streamline weights. If an elevated streamline count (for whatever causative bias) was not supported by the image data, then those streamlines should be down-weighted in that subject, and hence the sum of streamline weights would not change. What makes the situation more complex is considering:
The effect of regularisation within the SIFT2 solver;
The prospect that that elevated streamline count within the pathway of interest may not be just because there’s an isolated elevation of streamline count within that pathway, but because streamlines are traversing that pathway instead of adjacent pathways. So the total fibre density encoded within the image data is comparable across subjects, the total number of streamlines in that general region of the brain is comparable between subjects, it’s just that more streamlines within that general region are being ascribed to the pathway of interest rather than not.
I would also contemplate the effect of intracranial volume carefully. For instance, if you include ICV as a nuisance regressor in a GLM, does that gobble up the negative association between your behavioural measure and FBC? I would not think that minor differences in ICV would drive T2 differences of sufficient magnitude to influence FBC (since it does rely on AFD, which in turn is sensitive to T2).
One way might be to keep streamline numbers identical when extracting pathways after sift2, although it has its drawbacks.
If you wanted to attempt that path, I think what you would actually want is an equivalent number of streamlines within the pathway of interest in the concatenated whole-brain tractogram, which is more difficult again :-/
The first thing I would suggest is using a more dense whole-brain tractogram and abandon the targeted tracking. While I’ve presented the combined-whole-brain-targeted-tracking as a hypothetical solution to the problem of streamline discretisation effects in very small bundles, it does act in tension with the SIFT2 regularisation. If you can get enough streamlines within your pathway of interest without using targeted tracking, that would be preferable in that respect, and reduce the complexity of the machine you’re trying to debug.
What’s not shown here is the magnitude of the counter-intuitive effect relative to the variance in the data. While I’ve not interrogated it super-extensively, I do know that the variance in connection density estimates is a lot larger than would be desired for experiments such as these, and for minor bundles it can be very large indeed. So it’s possible that observation of the opposite of the expected effect is just by chance because you’re down within the noise.
Running FBA on your cohort would certainly be interesting. While FBC may physically be the measure that most appropriately captures your property of interest, being endpoint-to-endpoint connection density, I do believe that FBA has considerably less intrinsic variance, since it doesn’t rely on subject-specific tractography (I’ve just never gotten around to testing that hypothesis).
If continuing with the combination of targeted tracking & whole-brain tracking, you could try decreasing the strength of the regularisation. This will give streamlines greater flexibility to obtain small / large weights relative to their neighbours, and improve the fit to the model data; but be wary of individual streamlines obtaining huge weights, which has a comparable effect to using too few streamlines.
If you really want to get neck-deep in trying to understand this stuff, consider this.
Imagine that for those with the behaviour expected to correlate with increased FBC, the AFD along that pathway is elevated compared to others. Now in the iFOD2 algorithm, there is a minimum FOD amplitude threshold applied, such that directions for which the amplitude is lower than that threshold are not considered. If the AFD of a lobe is larger, then a larger portion of that “lobe” is above that threshold; whereas for a subject with a very small AFD, e.g. with a peak amplitude only just above the threshold, the FOD amplitude exceeds the threshold only for a tiny range of angles. These are the samples that are used for determining streamlines trajectories. So a set of streamlines within a dominant WM bundle with large AFD may exhibit orientation dispersion greater than that of a non-dominant WM bundle with small AFD.
So if an AFD elevation w.r.t. your behavioural measure were present within that pathway, but constrained to just your pathway of interest and not the surrounding WM, this could result in more streamlines straying outside of the pathway of interest during propagation, intersecting some other structure, and not being attributed to your pathway of interest, hence leading to a negative correlation with FBC.
See?! It was @jdtournier’s fault all along.
There’s a bunch of experiments that could be done here to try to diagnose; things that I’ve been thinking about for the last ~ 8 years but never committed to doing. So try a couple of things if you can, and see how invested you are in interrogating further.