Dear Donald,
Thank you very much for the fast reply and the helpful comments!
Please see inline response below.
Best regards,
Andreas.
MCLAREN, Donald schrieb:
> Andreas,
>
> Glad to see your using GLM Flex. Please see my comments below.
>
>
> On Wed, Oct 10, 2012 at 11:03 AM, Andreas Hahn
> <[log in to unmask]> wrote:
>
>> Dear Donald and SPM-experts,
>>
>> I have two questions regarding the GLM flex:
>> - To get used to the tool I compared the results of a 2x2 flexible factorial
>> (+ the subject factor since the second one is within-subject factor) in SPM8
>> with the results from the GLM flex. Interestingly, the result from GLM flex
>> is very different from the standard SPM8 analysis AND similarly different
>> from the SPM computation which was created by GLM flex (ComptOpt=1). I was
>> wondering why this differs from the latter analysis since only the final
>> contrast is created "manually" in SPM8. I understand that the standard SPM
>> analysis is slightly different from the SPM computation by GLM flex due to
>> modeling of the error terms.
>>
>
> Let me clarify the three models:
> (1) SPM8
> (2) GLM Flex
> (3) SPM8 called from within GLM Flex
>
Exactly.
> #1 and #3 should be identical as they use the same commands. If you
> are finding that they are different, please send me the 2 SPM.mat
> files and I'll track down the differences in the model that led to the
> results changing.
>
> The results between SPM8 and GLM Flex can be quite different. The
> largest differences occur when you use a contrast that is NOT valid.
> Specifically, comparisons of between-subject effects are NOT valid and
> that is where the greatest difference occurs. In GLM Flex, these
> contrasts are valid and have been compared to both 1- and 2-sample
> tests and the results are identical.
>
Right, #1 and #3 are the same, but #2 differs. So I was wondering if the
between-group contrast for the model above (see also attached design
matrix) is actually valid (comparing controls vs patients)?
1 -1 0 0 ones(1,15)/15 -ones(1,16)/16
and similarly is the contrast valid to test for differences between the
conditions?
0 0 1 -1 zeros(1,31)
>
>
>> - Now I would like to include a third factor (also 2 levels) and run a 3-way
>> interaction (which if I understood correctly is not possible in SPM8).
>>
>
> Correct.
>
>
>> The problem is that the factor matrix now has 5 columns (although the first
>> and last columns are identical) which gives an error.
>>
>
> I'll look into the first and last columns being identical. It might
> take a week or so, as I am travelling.
>
Great, thank you! I think this was set in RunSPM8ana.m, line 108 (if
that saves time for you).
> Leaving out the SPM
>
>> computation avoids this error, but I am not sure how to set the contrast for
>> the interaction (see attached design matrix):
>> -- the first gives an empty file:
>> I.Cons(1).c = [zeros(1,6)] 1 -1 -1 1 -1 1 1 -1 zeros(1,31)]
>> -- the second would give a result - but then I am still stuck with the very
>> first problem that GLM flex was different from the SPM analysis:
>> I.Cons(1).Groups = {7 8 9 10 11 12 13 14}
>> I.Cons(1).Levs = [2 2 2]
>>
>
> The second contrast is correct. What is the issue?
>
Since model #2 above was different from #1 and #3, I am not sure anymore
which one is correct. From the GLMflex Intro and your explanation above
it seems that GLMflex models the error term more accurately?
Great that the second contrast is correct but why does the first one
yield no result? (After having a hard time I feel now somewhat more
comfortable with contrasts like the first one).
>
>> Thank you for your help and best regards,
>> Andreas
>>
>> --
>> Andreas Hahn, MSc.
>> Functional, Molecular & Translational Neuroimaging
>> Department of Psychiatry and Psychotherapy
>> Medical University of Vienna, Austria
>> Phone: +43 664 8001662002
>> Email: [log in to unmask]
>> Web: http://www.meduniwien.ac.at/neuroimaging/
>>
>>
>
>
>
--
Andreas Hahn, MSc.
Functional, Molecular & Translational Neuroimaging
Department of Psychiatry and Psychotherapy
Medical University of Vienna, Austria
Phone: +43 664 8001662002
Email: [log in to unmask]
Web: http://www.meduniwien.ac.at/neuroimaging/
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