Thank you, your reply was very helpful.
I have one more specific question. How is the variance of the "group-level
contrast map" estimated in the RFX and WRFX cases (to be used for a t-test
or F-test)? Is it simply the sample variance of the lower level contrast
maps stored in "ces.nii" files?
Thanks,
Gabriel
On Mon, Mar 14, 2011 at 10:19 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:
>
> 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://s pdb.set_trace()
>
> urfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt<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
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
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