Hi Darren
> I have read through the list but still have a question about FSLVBM and setting up a proper model. My understanding is that the gray matter data are modulated by the Jacobian, but that the recommendation is that a covariate for total intracranial volume is not necessary in the analysis. I'm not sure I understand why. Does the Jacobian include both affine and non-linear aspects of the normalization? If so wouldn't modulating by the affine scaling mean that size differences would not be accounted for between subjects any more?
I haven't heard the recommendation that covarying for total
intracranial volume (TIV) isn't necessary, at least in regards to the
modulation issue. TIV is really just a global effect (1 number per
subject), as opposed to the modulation, which is voxel-specific.
I.e., they're controlling for different things.
In my experience including TIV almost always accounts for a decent
amount of variability; and, generally speaking, if I have an effect
that can be explained by TIV, that's not really what I'm after. So I
think it's generally a reasonable thing to include (at least to the
degree that it's a reliable estimate). Although, like anything, no
doubt it depends on the particular question being asked...
All that being said, I'd be very interested to hear other people's opinions...
> A second question is whether FSLVBM can be used on white matter? If so would it just be a matter of changing the Template specification at the top of the fslvbm_2_template script, and then making sure files were named appropriately through, e.g., WM for GM in file names?
(I'll have to leave that for someone else.)
Hope this helps,
Jonathan
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