Dear Tom
Thanks very much - that has definitely cleared up my main point and
thanks for explaining it so clearly.
I'm still not clear about the thresholding options though. In SPM2
you have to threshold the whole-brain before you can select SVC, and
then it seems that the SVC only applies to
supra-(whole-brain)-threshold voxels within the ROI - i.e. the
ultimate mask is the intersection between the initial whole-brain
threshold, and the ROI, not the ROI per se. The analysis mask is
determined by both the threshold and the ROI that you choose (hence I
thought that doing the whole thing through an explicit mask in the
model might be better). This is, as you say, why I get different
voxel counts depending on whether I apply my ROI after thresholding
the brain at 0.99, or prior to any thresholding.
So, is there an accepted whole-brain threshold that most people use
prior to applying SVC? 0.99 seems to be closest to what,
intuitively, I thought the SVC should do (i.e. correct for every voxel
within the ROI), but I've spoken to some people who use different
values.
Thanks again,
Susie
>
> I would have expected that you have identical voxel counts; I can only
> assume that in the 2nd instance, ROI as explicit mask, you're including some
> voxels with values less than 0.99 (and hence 122673 > 121424).
>
>
> > Why does the SVC button only look at voxels which already
> > exceed an (arbitrary) threshold? Is there a recommended whole-brain
> > threshold to apply before using the SVC button, and/or is it ok to set
> > this as near to 1 as possible?
> >
>
> There are two different issues wrapped up here: One is how the analysis
> mask is determined... either with an analysis threshold (e.g. .99) or via an
> explicit mask constructed manually (somehow) (you can also do the both, too,
> you know);
>
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