What is the range of FD value and FC value?Like FA(fractional anisotropy),It ranges from 0 to 1.
It’s not that simple, there’s no hard limits like there might be for FA. In general, FC should be around 1±20% (it’s a scale factor), and FD tends to be between 0 & 0.3 or so, but it might go quite a bit above that for various reasons.
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While FC should be 1.0 ± maybe 0.2, log(FC), which is calculated within the example pipeline and for which statistical inference is recommended over FC itself, should have values of 0.0 ± 0.2.
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FC cannot drop below 0.0 as long as your non-linear transform is diffeomorphic. Note also that this is requisite for the calculation of log(FC). Following the logarithm transform, there is theoretically no lower or upper bound on what the values could be, but if you’re dealing with data of the same species, of comparable age, it would seem intuitively unusual to have expansion / dilation factors of e.g. 10% or 1000%.
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For FD, if you take your single-fibre WM response function, and use it to deconvolve a voxel containing a single WM fibre bundle of comparable DWI signal intensity, and then perform the explicit FOD segmentation process within the
fod2fixelcommand, you should obtain a value of FD of around 1.0. It’s possible to obtain values of FD of greater than 1.0 as any single WM voxel may exceed the “fibre density” corresponding to that calculated from those image voxels used to derive the WM response function. This is why we’re always careful to never refer to these as “volume fractions”. Seeing values as high as 1.5 is not unusual. If there is no fixel in subject space that maps to a fixel in template space, then the value of FD for that template fixel will be 0.0. It is however not possible for there to be “negative fibre density”. By default the threshold applied during fixel segmentation to determine whether or not an FOD lobe results in a discrete fixel is based on peak amplitude rather than integral on the sphere (which is what determines FD), so while there will be some non-zero minimum value of FD for segmented fixels, I don’t know off the top of my head exactly what it is.
I found FD values for the two subjects I selected ranged from 0 to 1.5(1.47324169,1.49300857,1.48639834,1.49554777).(I really want to know why it is so much higher than what you said between 0 and 0.3. Do you have any relevant literature that you can recommend to me?)
I suspect what’s happened here is an erroneous conflation between the fixel-wise FD measure and the intensity of the WM l=0 term of the spherical harmonic expansion (the “WM density” image you see if you load an ODF image as the main image in mrview). There is a factor of sqrt(4pi) difference between these two. So for the example I provided earlier, where you de-convolve a single-fibre WM voxel with a single-fibre WM response function of equal intensity, the value of the WM ODF l=0 image will in fact be ~0.282, whereas the value of FD of the segmented FOD lobe will be 1.0.
And the FC values for the two subjects I selected ranged from 0.6 to 1.6[Isn’t that a bit different from what you said: 1±20% (0.8-1.2)].
If you are quoting extreme values (i.e. the maximal values across all fixels for any particular subject), this isn’t problematic I don’t think. But “healthy variation” within major white matter bundles would be of the order of 20% as “typical values” rather than extrema.
How can I visualise the fixel-fixel connectivity matrix generated in Step21?
No way currently. The construction of this format is pretty new, and for the vast majority of applications there’s no need to interact with these data visually, so there has been no motivation for me to implement any kind of visualisation mechanism.
Rob