Hello Afni experts,
I am kind of new to neuro-imaging and Afni, so please pardon these many basic questions.
I ran the proc script with both FDR and 3dClustSim and got the results attached to stats_REML. I am now looking at the stats_REML data in the GUI.
My questions:
1) Is the p value under slider bar corrected or uncorrected?
If I didn't run the Monte Carlo simulation with 3dClustSim, that would be the uncorrected p value. Since I ran it and the results were attached to the stats_REML data, that should be the corrected p value. Am I right?
2) If it is the uncorrected p, and I want to use the FWE-corrected p (height thresholding) before applying cluster-size threshold (extent thresholding). What should I do? Where can I get the FWE-corrected p value?
3) The other way around: If it is the corrected p, and I want to use the uncorrected p before applying cluster-size threshold. Where can I get the uncorrected p value?
4) Related to questions 2) and 3), which way is recommended? Is it better to go with the uncorrected or corrected p at the voxel level?
5) The last column in the Cluster table is for Alpha value. Is this Alpha the Alpha calculated when I run 3dClustSim or it is something different?
Also, I understand that we have to find clusters that produce Alpha <= .05? In my results (after doing CLUSTERIZE), I obtain Alpha > .10 for all clusters in the list even when p was set to .05. What should one report in this case?
6) In the cluster results for one run, I see this line: "Min FDR q in threshold = 0.62: True detections are rare or weak". For another run, I got "Min FDR q in threshold = 0.60: True detections are rare or weak". People typically use a cut off q value of .05. Does this mean FDR is too conservative and I should not use it to look at the change between the 2 runs? or perhaps I can just set FDR = 0.62 for both runs and compare the activation anyway?
I very much appreciate your time clarifying these points.
Duong