Hi Dough,

- I believe the 3dANOVA* programs handle multiple observations,
but 3dttest++ does not. So using 3dANOVA might be an option,
but it does not have any -Clustsim option.


- The clustsim output is a cluster table, much like what would
come from 3dClustSim, such as this class example from AFNI_data6:
AFNI_data6/FT_analysis/results.clustsim.05/files_ClustSim/ClustSim.ACF.NN1_1sided.1D.

The row is based on an uncorrected p-value threshold, listed
in the first column. The column is based a corrected p-value
threshold, listed above the dashed lines. The combination
would be required cluster size.

For example, using an uncorrected p-value of 0.001 for the
voxelwise threshold, to get a corrected p-value of 0.05 at
the cluster level would require a minimum cluster size of
22 voxels (from 21.9 in the table).


- Such a cluster table is produced by 3dttest++ -Clustsim,
though it is up to you to apply the threshold/cluster step
(it does not assume which p-values to apply).


- The thresholding and clustering is applied to a t-stat or
z-score volume. The mean volume would probably be used for
colorization, showing the effect size.


- The choice of ETAC is up to you. The ETAC output is not
a cluster table but a mask of surviving voxels.


- It is appropriate to specify your group mask in the
clusterizing operation (e.g. to 3dttest++). It is nice to
generate unmasked results as well, for review.


- The -ACF option applies when you have computed ACF
estimates, probably at the single subject level, from
afni_proc.py, and when you are applying them in 3dClustSim.
Previously (in your post), 3dClustSim was not mentioned.


- There is no default threshold, except in the ETAC case.
But a corrected p of 0.05 is the most common.


- rick