Type of thresholding used for alpha in Cluster Results window


a quick question here. What is the thresholding scheme (1-sided, 2-sided, bi-sided) used for displaying the alpha values in the Cluster Results window? Given the rationale in the 3dClustSim help text, I would think it’s the 2-sided one, but I just wanted to make sure.

Perhaps I should also add that I am examining a Z-map obtained from 3dttest++ with the new option “-Clustsim”.

thanks in advance

Hi Giuseppe,

I ran a verification test of this last night. Running 3dinfo on
the output from the ttest command should show that it uses
all 3 types and all 3 NN options, i.e. all 9 cases are added to
the stats dataset. After that point, the afni GUI will apply the
appropriate results in the cluster report window.

  • rick

Hi Rick,

Alright, I see … if you check the “Pos?” box under the colorbar in the main AFNI window, in the Cluster Results window the 4th line from the top (“Alpha → Cluster Thresh”) gives cluster size thresholds that match indeed the values in the clustsim*1sided.1D file saved by 3dttest++ (with the option -Clustsim).

If you leave the option “Pos?” unchecked, instead, the cluster size thresholds reported in the Alpha line of the Cluster Results window match the values in the clustsim2sided.1D file (or the clustsimbisided.1D file, the values are often the same).

thanks for checking!


Glad it is working for you, and thanks for the

  • rick