Brian,
I'll answer your second question...
> 2) For determining the voxels that are "pooled" and enter the ReML
> calculation of hyperparameters, the code is somewhat hard to
> decipher. Is it correct to assume that the voxel is "significant"
> and enters "pooled" data (i.e. Cy) if:
>
> F(voxel) > F(p=0.001)
>
> where: F(p=0.001) is calculated using numerator and denominator
> d.o.f. as determined from design matrix (i.e. trace(X) and trace(R)
> respectively)
That's right.
> Also, is pooling "significant" voxels done for theoretical or
> computational reasons and would there be a reason not to just pool
> all in-mask voxels???
Theoretical/modeling reasons. I don't think anyone really believes
that the nonsphericity/covariance is homogeneous over the brain, so
the question is instead: If we have to assume a global covariance, for
which voxels do we want the global estimate be most accurate? SPM
says "we care about the voxels most likely to contain true signal,
those with P_F < 0.001 based on a preliminary OLS".
Honestly, I'm uneasy with a global covariance assumption. One small
thing I do to at least get a small sense of how this works, is that I
notice how many voxels are used in this estimate. In spm_spm.m,
around line 820 in SPM2 and around 860 in SPM5, I added the last line
below:
% normalize non-sphericity and save hyperparameters
%---------------------------------------------------------------
V = V*nScan/trace(V);
xVi.h = h;
xVi.s = s; % # vox contributing to Cy
and then, manually, after the analysis is complete, I look at
SPM.xVi.s. If it is really tiny (say less than 20) I might worry
about the quality of the covariance estimate (not enough data). If s
is really huge, I might also worry, as then huge amounts of the brain
(which are probably heterogeneous) are being pooled to determine the
global estimate.
Hope this helps.
-Tom
-- Thomas Nichols -------------------- Department of Biostatistics
http://www.sph.umich.edu/~nichols University of Michigan
[log in to unmask] 1420 Washington Heights
-------------------------------------- Ann Arbor, MI 48109-2029
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