Your AFNI is two years old, which explains the weird results: the old version of 3dLME only allows for pairwise comparisons! Update it first:

@update.afni.binaries -d

and rerun the analysis.

> The individual subject maps going into the 3dLME are beta maps - is that what you were asking?

No, that is not what I mean.

> The contrast t-test result of the 3dLME (contrasts 3 and 4) yield the same result - same t-values
> within the same voxels in the brain.

There are two sub-bricks in the output that are associated with each post hoc test. The sub-brick right before each t-stat is what I was asking: So is that sub-brick the same between post hoc tests 3 and 4?

Gang



Edited 2 time(s). Last edit at 04/07/2015 11:18AM by Gang.