3dttest++ -clustSim

Hello AFNI

Im running 3dttest++ with 2 independent samples. Im trying to use the -Clustsim option for the first time and I would like to have some help in the interpretation of the results. It seems that my script run correctly, I even get the message at the end " -Clustsim work is finished :slight_smile: " .
I have been reading that as a part of the results I should get a table to be able to define the cluster size but Im confused with this part. I don’t see any output with a table with the values and cluster size, in the output tempFiles I have FacevsShapes_ClustSim.0000.minmax.1D (from 0000 to 0023). How can I know my cluster size and the p-value?

Im very sorry in advance if I didn’t understand this part correctly. and I really appreciate the help

Are there any files of the form *NN1_bisided.1D, for example? Those are the Clustsim results.

It looks like you might have also used -ETAC, which might be confusing the issue. Did you want to use -Clustsim or -ETAC for the correction?

  • rick

I don’t get any files of the form *NN1_bisided.1D. Im not sure what Im doing wrong

Here is my command


3dttest++ -mask ${TEMPLATE}/JGMask/GM2mm_WFU_Mask.nii.gz
-prefix ${EMOTIONDIR}/group_results/AngervsNeutral_noHDRS_WFU_GM
-prefix_clustsim AngerNeutral_noHDRS_ClustSim
-tempdir ${EMOTIONDIR}/group_results/tempFiles/
-Clustsim 24
-covariates /rcc/stor1/projects/GerDep/Luisa/scripts/Preprocess/task/group_stats/covariates_3dttest.txt"[0,1,2,3,5]"
-center SAME
-setA HighGrief 230 ${EMOTIONDIR}/230_011116/results_skullstrip/anger_gr_neutral.nii \ (+20 more subjects)
2…n ${EMOTIONDIR}/230_011116/results_skullstrip/anger_gr_neutral.nii \
-setB LowGrief 172 ${EMOTIONDIR}/172_120916/results_skullstrip/anger_gr_neutral.nii \ (+20 more subjects)
2…n ${EMOTIONDIR}/230_011116/results_skullstrip/anger_gr_neutral.nii \

Hmmm, I would have to look through the code and to some testing to see how it handles all of those possible directories. $TEMPLATE is used, $EMOTIONDIR in the -prefix, then separate -prefix_clustsim and -tempdir options.

Just to be simple, I suggest setting it up to run from the ${EMOTIONDIR}/group_results directory, and then not having any paths for the output.

Does that seem reasonable?

  • rick

it works now!!!

I got the tempFacevsShapes_042220_ClustSim.CSimA.NN1_1sided.1D output files

Thank you so much Rick

Great, thanks for the update!

  • rick