yes, that is correct

Gabriel Go.Es. wrote:

Dear Doug,

I really appreciate all your answers, and to be sure that I understood the reasoning for setting the contrast for the interaction effect.

Let's assume that we have 9 groups (two factor, with three levels each).

G1-left G1-right G1-ambi G2-left G2-right G2-ambi G3-left G3-right G3-ambi

[1 -1 0 -1 1 0 0 0 0]/2 [1 0 -1 -1 0 1 0 0 0]/2 [1 -1 0 0 0 0 -1 1 0]/2 [1 0 -1 0 0 0 -1 0 1]/2

However, if we have 8 groups (two factors, one of them with 4 levels)

G1-male G1-female G2-male G2-female G3-male G3-female G4-male G4-female

[1 -1 -1 1 0 0 0 0]/2 [1 -1 0 0 -1 1 0 0]/2 [1 -1 0 0 0 0 -1 1]/2

Is this correct?

Thank you very much in advance, Gabriel

---

Date: Wed, 9 Mar 2011 22:22:18 -0500 From: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glm question

two row contrast matrix

[1 1 -1 -1 0 0] [1 1 0 0 -1 -1]/2

1st row test for a difference bet G1 and G2 2nd row tests for a difference bet G1 and G3 Note that you don't need to test G2 vs G3 (that is implied by the other two tests).

doug

On 3/9/11 7:33 PM, Gabriel Go.Es. wrote:

Thanks a lot,
 just one another question Doug,
how to set an ANOVA for group differences??'

Gabriel





> Date: Wed, 9 Mar 2011 17:52:03 -0500
> From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> To: gabriellbk@hotmail.com <mailto:gabriellbk@hotmail.com>;
freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] glm question
>
>
>
> Gabriel Go.Es. wrote:
> >
> > Thank you so much, Doug
> >
> > I've check at your update and saw that this contrast has to be
/2,
> > wich I guess means 0.5 instead of one to keep the scale right?
> Yes.
> >
> > and the contrast for me, would be something like:
> > Let's suppose
> > group1_males
> > group1_females
> > group2_males
> > group2_females
> > group3_males
> > group3_females
> > for differences between males and females (males > females)
> > regreessing the efects of group would be:
> > [0.333 -0.333 0.333 -0.333 0.333 -0.333]
> Correct
> > differences between group1 & group 3 regressing the effects of
gender:
> > [0.5 0.5 0 0 -0.5 -0.5]
> Correct
> > and the differences between males and females for a single
group can be:
> > [1 -1 0 0 0 0]
> > am I right???
> Yes
> > but I don't yet figure out how to set a difference from 0 in
any of
> > the group means (to meassure the effect of group), nor the
interaction
> > between group and gender, and that's because my model is not
like the
> > one from the example,
> Try using
> [1 -1 -1 1 0 0]
> [1 0 0 0 -1 1]
>
> This is a single matrix with two rows. The first row tests for an
> interaction between G1/2 and M/F. The second row tests for G1/3
and M/F.
> Note that you don't need a third row.
>
> >
> >
> >
> >
> >
> > > Date: Wed, 9 Mar 2011 14:52:37 -0500
> > > From: greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
> > > To: gabriellbk@hotmail.com <mailto:gabriellbk@hotmail.com>
> > > CC: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
> > > Subject: Re: [Freesurfer] glm question
> > >
> > > That contrast is wrong. I've updated this page with the
correct contrast
> > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf6G0V
> > > which is:
> > >
> > > |+1 -1 0 -1 +1 0|
> > > |+1 0 -1 -1 0 +1|
> > >
> > > This is an F-contrast (two rows). The first row looks for a
difference
> > > between L and R for M and F (ie, a simple interaction
between LR and
> > > MF). The second row looks for a difference between L and A
for M and F.
> > > If either of these subcontrasts shows an effect, then there
is an
> > > interaction.
> > >
> > > doug
> > >
> > >
> > > Gabriel Go.Es. wrote:
> > > >
> > > > Dear FreeSurfer experts,
> > > >
> > > >
> > > >
> > > > I'm doing some group analyses and I'm a little stocked
with this:
> > > >
> > > > I have Six Groups (2 Factors, one with three levels and
the other one
> > > > with two levels), and one covariate. I don't know the rule
for
> > setting
> > > > the contrasts for an ANOVA and for the interaction between
the two
> > > > factors regressing out the covariate. I've checked at the
FS wiki and
> > > > found the following contrast for six groups (two factors)
and zero
> > > > covariates.
> > > >
> > > >
> > > >
> > > > Contrast 6 gender-x-handedness.mtx (interaction between
gender and
> > > > handedness)
> > > >
> > > > [0.333 -0.333 -0.333 0.333 0.000 0.000 0.000 0.000 0.000]
> > > >
> > > > [0.000 0.000 0.000 0.000 0.000 0.333 -0.333 -0.333 0.333]
> > > >
> > > >
> > > >
> > > > I don’t understand the rule that has been followed.
> > > >
> > > > Can any one help me with this?
> > > >
> > > >
> > > >
> > > > Bests,
> > > >
> > > > Gabriel
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> >
------------------------------------------------------------------------
> > > >
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> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > >
> > >
> > >
> > > The information in this e-mail is intended only for the
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> > whom it is
> > > addressed. If you believe this e-mail was sent to you in
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> > the e-mail
> > > contains patient information, please contact the Partners
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> > HelpLine at
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@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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>