Faulty FDR, Help needed running 3dClustsim and 3dttest++

AFNI Message Board
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Hi afni experts, afni newbie here. I am trying to run 3dClustsim on a dataset where I’m also using 3dttest++ to create functional overlays for a group analysis. I’m doing this because the false discovery rate is not working properly in my version of afni for some reason (I’m using afni Bootcamp on my pc). To elaborate, the q value adjusts itself only to a point but after I raise the T-threshold slider past a certain point it stops adjusting itself. I was told to run 3dClustsim on my dataset to compensate for this, but I am unsure how to execute this in the terminal, and I could really use some help with working this out. Could someone please demonstrate how to accomplish this? Do I need to run 3dClustsim before or after 3dttest++, or run them simultaneously?

Thank you in advance,

Jen

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To elaborate, the q value adjusts itself only to a point but after I raise the T-threshold slider past a certain point it stops adjusting itself.

That is most likely due to the fact that there are not many voxels with high t-stat values.

Do I need to run 3dClustsim before or after 3dttest++, or run them simultaneously?

A simpler approach is to rerun your original 3dttest++ script by adding option -Clustsim. Also read the 3dttest++ help for details regarding the option -Clustsim.

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Thank you for your response, Gang. I added the -Clustsim option to 3dttest++ and ran the script. It created 3 output files; the brik and head files and a resid.nii file. However, now the terminal is asking me to input ‘t-test randomsign’. I’m not sure what to enter here, and regardless of what I enter nothing happens. When I try to close the terminal I get a prompt that there is still a process running in the terminal. What should I do at this point? I have the output files, but this prompt is making me think that there is additional step(s) to do and/or that the 3dttest++/Clustsim operation is incomplete.

Jen

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I can only think you have an out-dated version of AFNI. What the output of the command afni --ver ? If the version number is below AFNI_17.1.00, you need to update your AFNI binaries.

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I’m currently running AFNI_16.2.13…I guess that explains it. I’m working with the precompiled binaries on linux_fedora_21_64, from Aug 25 2016. Thanks for pointing this out, Bob.