Hi Gabriel,
for mri_glmfit, W = diag(sqrt(1./yffxvar)), ie, it is a diagonal matrix
where each element is the square root of the inverse of the variance
from the lower level. This changes the equation from a simple ordinary
least squares into a weighted least squares (though not quite a true
mixed-effects analysis).
There are not explicitly nuisance regressors in the B matrix. The B is
the matrix of regression coefficients ("betas") based on the solution to
the forward model y=X*B (B=inv(X'*X)*X'*y). So the frames in B depend on
the design matrix which depend on how you've set up your FSGD (or if
you've entered the X matrix explicitly).
I don't have another manuscript, but there is a lot of detail in the
tutorial slides
ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt
doug
Gabriel A. Tobon wrote:
> Hello Freesurfers
>
> I would like to run a specialized group GLM analysis on the volume
> using estimates from the individual subject analysis in Freesurfer as
> summary statistics. I would like to learn a little more about how
> this estimation is done before doing so. I have looked at the
> documentation for "mri_glmfit" and the following tutorial:
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial
> I also have your 1999/2003 manuscripts on "Signal Processing and
> Statistical Analysis for Event-Related fMRI" and "fMRI Analysis 101 -
> Univariate Analysis," but I am not sure if the method has been updated
> since then.
>
> * I noticed there is a weight matrix (W) described for "mri_glmfit"
> command. How is this derived and used? I can't find more information
> about it in the documentation/mailing list.
> * How are the nuisance regressors organized in the B matrix? I assume
> the conditions are first? What are the following regressors?
> * Do you have a similar manuscript that describes just how group
> analysis is implemented in FsFast?
>
> Thank you for your time and help!
> Gabriel
> ------------------------------------------------------------------------
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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