I'm trying to use the PET "Compare-populations: 1 scan/subject (two sample
t-test)" model.
The confusing part is when I get to the non-sphericity questions.
It's also not clear to me that spm_spm_ui('Files&Indices',...) is
correctly computing the factor indices.
I have two groups, of size 15 and 10. This produces a 25x4 factor
matrix, "I". The last two columns are all ones. The first column,
representing "subject" according to D.sF, is of the form
[1:15, 1:10]'
The second column, representing "group," is
[ones(15,1); 2*ones(10,1)]
Subsequent code in spm_spm_ui seems to interpret the first column
literally as factor levels for factor "subject." But that doesn't seem
right. First, I don't see why "subject" is a factor with distinct levels
in a two-sample t-test (in the context of subjects drawn from two
populations, with inferences to be drawn at the population level).
Second, the code seems to identify subject 1 of group 1 with subject 1 of
group 2, and on up to subject 10 of group 1 and 2, when in fact these are
distinct subjects. This then leads to what appears to be incorrect
specification in the non-sphericity module. (Since the subjects are
distinct, there are no repeated measures, but of course the two groups can
have different variances.)
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