AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

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.

Sincerely, AFNI HQ

History of AFNI updates  

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October 31, 2017 04:31PM
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
Subject Author Posted

p and q values under the Slider bar / alpha in the Cluster table

dlhuynh October 31, 2017 04:31PM

Re: p and q values under the Slider bar / alpha in the Cluster table

rick reynolds November 03, 2017 09:25AM

Re: p and q values under the Slider bar / alpha in the Cluster table

dlhuynh November 03, 2017 04:01PM

Re: p and q values under the Slider bar / alpha in the Cluster table

rick reynolds November 09, 2017 11:03AM