James,
> Am I understanding this correctly?
Yes you're understanding it accurately.
> If so, why would the default change?
The default setting for the threshold slide bar on the AFNI GUI is two-sided, and the Clusterize button is tied with the threshold slider bar. So, to be consistent it would be better to set the default for 3dClustSim to be the same. Such consistency is important in case the user is not aware of the issue.
Another possibility is to change the default setting on the GUI from two sided to one-sided.
Gang
Edited 2 time(s). Last edit at 12/18/2014 10:01AM by Gang.
