We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
The suggestions you're referring to in the 3dFWHMx help are for the situation when you use the residuals from the individual subject analysis as input to estimate the ACF parameters. For your case, you may try something like this with your group analysis residuals (e.g., filename group_residuals) as input: