I am getting different results from 3dttest++ paired sample test and 1-sample test using differences between conditions. The subtraction method gives me a large cluster that is only present in the paired test when I significantly lower the threshold.
The reason I performed a 1-sample test using subtraction is because I am planning to run a paired test using covariates, where the covariates are different for each condition. Based on this explanation from 3dttest++ I would expect the two methods to be equivalent. Can someone help me understand which method I should be using in this case?

“++ If you want to use different covariates for setA and setB in the
paired test, then you’ll have to subtract the setA and setB
datasets (with 3dcalc), and then do a 1-sample test, using the
differences of the original covariates as the covariates for
this 1-sample test.
++ This subtraction technique works because a paired t-test is really
the same as subtracting the paired samples and then doing a
1-sample t-test on these differences.”

What sort of differences are you seeing? Is it basically truncation
errors? I ran such a test and that is all I saw. The results should
be almost identical, but they will not be exactly so.

Aside from the issue of inconsistency between one-sample and paired t-test:

the covariates are different for each condition

It would be more appropriate to use linear mixed-effects model to handle the cross-subject variability in terms of the covariate effect. Check out Example 2 in the help of 3dLME.

The results look somewhat similar. A cluster of 140 voxels in one version is 30 voxels in the other. Some clusters also shifted location (i.e by 10 mm). Is this normal?

Thanks again,
Melissa

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National Institute of Mental Health (NIMH) is part of the National Institutes of
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