Hi-

Typically, one inputs the residual time series from single subject processing into 3dFWHMx, to estimate the scale of the spatial extent of noise (the output ACF parameters describe a function that fits this shape well; for a long time, it was just a Gaussian shape, but a paper made the useful point that that doesn't appear to be a good approximation in practice, so AFNI has changed the shape for fitting the noise). Then, for a given study of N subjects, one typically has N sets of ACF parameters---one from each subject's residual time series (errts*, in afni_proc.py outputs). Typically, we average each ACF parameter across teh group, because they are quite similar anyways in practice for subjects acquired on the same scanner. Then we take that final, single set of ACF parameters, and run 3dClustSim using that.

In your case, you are using just the residuals from 3dLME. I am not sure what those look like; I suspect that those might not be what you want to use here.

What is the output of:

3dinfo -n4 LME_3Grp_covar_resid.nii.gz

?

Also, it appears that your voxel sizes are: 1.50x1.50x1.50 mm^3. That is pretty small for FMRI, in general. A typical FMRI voxel would be, say, 3.0 mm isotropic, and so that would be a factor of 8 difference in volume between those---so, you would expect clusters that are about 8x as large in your case as if you were processing at 3mm. Even the difference between 1.5mm isotropic and 2.0mm isotropic is notable, with the latter being 2.4x bigger.

But the first issue may be a bigger consideration here.

--pt