If x1 and x2 are the same thing, then the equation is non-invertible. If they are the not the same variable, then there is no problem. QDEC computes all the contrasts for you (but excludes contrasts with nuisance variables)
doug

On 8/13/13 3:03 PM, ye tian wrote:

Dear Doug,

I am afraid that I still don't understand why a variable can not be "covarying" and "nuisance" simultaneously. 

If variables x1 and x2 are covarying, they both go into the model 

y = b0 + x1*b1 + x2*b2 + err

Is this correct?

Nuisance, however, is related to the contrast, i.e., test hypothesis. If x2 is nuisance, then 

(1 0) * (x1 x2) = 0 

Is this correct?

Otherwise, how does one specify the contrast matrix in Qdec?

Thank you very much!

Sincerely,

Ye

On Tue, Aug 13, 2013 at 12:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Ye, don't select the same factor as nuisance and covariate. It will
result in an error for sure. The difference between a covariate and a
"nuisance" factor is purely conceptual. By calling something a nuisance
you tell QDEC not to create a contrast related to it.
doug

On 08/13/2013 02:09 AM, ye tian wrote:
> Dear Freesurfers,
> I have a question concerning the "nuisance factors" in the qdec
> dialogue. Suppose I have two independent variables x1 (discrete) and
> x2 (continuous), and only one observable y. I choose "Discrete (Fixed
> factor) = x1", "Continuous (covariate) = x2".
> If I further chose "Nuisance factor = x2", does that imply that
> 1) my contrast matrix is (0 1)
> 2) null hypothesis: Y is independent of x2
> Thank you very much!
> Sincerely,
> Ye
>
>

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