The t is correct. When the contrast matrix only has one row, then the F
is just an unsigned t. I don't know anything about SPSS so I can't tell
from what you have sent whether it is the same model or not. Try to get
SPSS to output the design matrix. Did you try the matlab code below?
On 01/29/2015 01:40 PM, maaike rive wrote:
> Hi Douglas,
>
> I checked but as far as I see it I used the same models. I attached
> the SPSS model and output as wel as the FSGD file and contrast file
> (to test a diagnosis x age interaction). Now that I come to think of
> it, I think the reason for the discrepant findings is that I used a
> t-contrast instead of an F-contrast for the interaction in Freesurfer.
> Apologies I did not think about this earlier. But maybe there is
> something else I did completely wrong.
>
> What do you think?
>
> If it is indeed the t vs F contrast, than how should I specify that
> the contrast is an F-contrast? Is it ok to just add another line to
> the contrastfile (so
> 0 0 0 0 0 0 0 0 1 1 1 1 -1 -1 -1 -1
> 0 0 0 0 0 0 0 0 -1 -1 -1 -1 1 1 1 1)?
>
> Thanks again,
>
> Maaike
>
> > Date: Mon, 26 Jan 2015 11:23:59 -0500
> > From: gr...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] average values per cluster
> >
> >
> > We get these kind of reports occasionally. When I ask people to confirm
> > that they use exactly the same design matrix in SPSS, I never hear
> back,
> > so I assume that it gets resolved. So please check. The other thing you
> > can do is to run in matlab, something like
> >
> > cd glmdir/contrast
> > X = load('Xg.dat');
> > y = load('ocn.dat');
> > C = load('C.dat');
> > [beta rvar] = fast_glmfit(y,X);
> > [F p] = fast_fratio(beta,X,rvar,C);
> > p will be the p-value
> >
> > If you used an unsigned cluster-forming threshold (ie, abs), then it is
> > possible that some of the voxels are pos and some are neg so that they
> > average out
> >
> > doug
> >
> >
> >
> >
> > On 01/26/2015 09:03 AM, maaike rive wrote:
> > > Dear Freesurfer experts,
> > >
> > > Sorry to bother you again, but I have two more questions about
> > > extracting (thickness/surface/GI) values from a certain cluster.
> > >
> > > As I understood, the abs.y.ocn.dat file gives the average values
> for a
> > > given significant cluster (e.g. a cluster where there is a
> significant
> > > AxB interaction).
> > >
> > > I may be completely misunderstanding things, but if I use these
> values
> > > in SPSS for further statistics and test the same interaction (AxB),
> > > than according to SPSS this interaction is /not /significant
> > > (corrected for the same covariates as in the FSGD file).
> > >
> > > Could you tell me what is going wrong here? I do not trust my
> results now.
> > >
> > > Furthermore, is it possible (and if so, how?) to extract the average
> > > values of exactly the same cluster, but in an independent group not
> > > used in the analysis, for post-hoc comparisons in SPSS?
> > >
> > > Thanks,
> > >
> > > Maaike
> > >
> > >
> > > _______________________________________________
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> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > 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
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> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
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> >
> >
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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