Hello,

There isn't a mask in your 3dClusterize command, was a mask already applied?

To do cluster correction, one usually runs:

3dFWHMx - to get blur estimates (3 ACF parameters) from the residuals
3dClustSim - to run Monte Carlo cluster simulations
(input is mask and ACF params)

Then choose an output cluster table for the preferred NN_level (NN1?) and test style (e.g. bisided).

From that table choose a row based on the uncorrected p-value that you are applying and the column based on corrected p (alpha) value that you are applying.


The way alpha values get reported from the afni GUI's clusterize report is because 3dFWHMx and 3dClustSim can be run automatically by afni_proc.py, with the output tables being stored inside the stats dataset. If you similarly stored the 3dClustSim results in the group analysis result, the afni GUI will show similar alpha values at the cluster level. 3dClusterize does not search for and report those alpha values.

But typically one just chooses and overall alpha value and therefore a minimum cluster size for correction at that level. Then the entire map would be corrected at the given alpha value.

Does that seem reasonable?

- rick