> When comparing these two models, I am wondering how to interpret voxels that were significant in the non-amplitude
> modulated analysis but non-significant in the AM2 analysis. In addition, I am wondering the reverse, how would I interpret
> voxels that were not significant in the non-amplitude modulated analysis but are significant in the AM2 analysis?
I would be a little careful about the comparisons. The demarcation between "significant" and "non-significant" results is like drawing a line in sand, which depends on some underlying assumptions about the adopted model. Without knowing the model specifics and the detailed results, it's hard to make accurate assessments about the comparisons between the two modeling pipelines. In addition, in the LME model at the population level as well as the AM2 approach at the subject level, linearity is implicitly assumed about the slopes. In addition, cross-trial variability is assumed to be negligible.
> My main point of confusion is that the variables in the amplitude-modulated analysis are demeaned within condition.
With the assumption that your LME model took the intercept effects (instead of the slopes) from the AM2 output as input at the population level, demeaning would be appropriate in the current context.
Gang