So for me it appeared in part to be an AFNI version issue. I checked and realized we were running a few versions behind the current build. So now the -clustsim flag is recognized by AFNI when I run it. However, I am running into a different error now.

The output .BRIKs containing the results of the group analysis as well as the residual file are created successfully, but the program fails when starting the clustsim portion, giving the following error:

FATAL ERROR: Option -setA (long form): need at least 2 datasets.

So, it would appear that upon reaching the clustsim portion of the analysis, it no longer recognizes the manner in which the ttest is set up. I am confused by this because if there was a problem with the way things were set up––btw, this is supposed to be an independent samples t-test, with 2 groups (unequal size) and covariates)––then wouldn't the output of the group analysis not be created either?

Any suggestions would be much appreciated.

Thanks,
Dominic