Dear Nocholas,
> My procedure is as follows:
> 1 scan/subject Ancova,
> (as only covariate I enter the GM-value given by Johns function
> in
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0010&L=spm&P=R36678)
> no global normalisation
> no grand mean scaling
> (because I understand that both global normalisation and grand
> mean scaling are unnecessary when using these GM-values as a
> covariate),
by the way, you can simplify the procedure by entering
'get_integrals(spm_get)', when SPM prompts for the values. An other
possibility is, to use no nuisance covariate at that point an select ANCOVA,
when asked for 'global normalisation'. The values, extracted by
get_integrals and this 'global normalisation' are highly correlated and the
results are (nearly) identical.
> Then I do not know how to proceed with threshold masking.
> John, you suggested using an absolute threshold of 0.05 if I don't
> do any global scaling.
> So what thresholding should I use here?
> absolute and if so, what value?
> or proportional and if so, what value?
In this model, you don't do any scaling, so you should use 'absolute' and
'0.05' as John mentioned in his previous mail.
> Global calculation:
> is mean voxel value correct?
You should select 'omit' when using the 'get_integrals' tool, and 'mean',
when using ANCOVA.
> I should add that I am planning to use FDR and Kalinas
> glm_specmask, later probably also ROIs, defined with the AAL
> brain in MRIcro.
That's fine.
Good luck,
Karsten
----------------------------------
Karsten Specht
fMRI Section
Department of Neuroradiology
Medical Centre Bonn
Spessartstrasse 9
53119 Bonn
Germany
Phone: ++49-(0)228/90 81-178
Fax: ++49-(0)228/90 81-190
E-Mail: [log in to unmask]
WWW: http://www.mcbonn.de/Praxis/praxis15/fmri1.htm
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