Hi everyone!

I’m relatively new to AFNI and I’m trying to run a -ClustSim analysis using 3dttest++. I just have a few questions about parameters for the simulations.

1) What is the recommended number of simulations? Running 1,000 simulations finished successfully after ~26 hours of runtime on our 2017 iMac with an i5 and 8GB of RAM. Our more recent run with 10,000 simulations has taken over 4 days so far and is only maybe half way finished (although I realized afterwards this may have been due to the computer going to sleep at some point). We have been changing the number of simulations by setting DAFNI_TTEST_NUMCSIM=10000. Is there an ideal number of simulations and/or perhaps a faster way to run them?

2) Does a simulation need to be run for each contrast in the data set? For example, we have multiple condition contrast files setup for each participant. Will each one provide a unique minimum cluster size as a result of simulations? Presumably the answer is yes since the mask and functional files show data from different conditions being contrasted, but in published papers that use this -ClustSim option I tend to only see a single minimum cluster size reported.


3) Should the functional files that are used in the 3dttest++ function be tlrc files or should they instead be spatially smoothed files? For example, we used the following code to turn our normal (‘tlrc’) files into spatially smoothed (‘ss’) files for each participant: 3dmerge -prefix WNss -1blur_fwhm 6 WN+tlrc. Which is better for -ClustSim?



Here is our current 3dttest++ code for one of the contrasts:

3dttest++ -ClustSim -prefix DN-Con-Results \
-mask /Users/mafernan_admin/Desktop/anova_TEST/mask_union+tlrc.HEAD \
-setA DN_Con MM03 "/Users/mafernan_admin/Desktop/anova_TEST/p03_DN+tlrc" \
MM04 "/Users/mafernan_admin/Desktop/anova_TEST/p04_DN+tlrc" \
MM05 "/Users/mafernan_admin/Desktop/anova_TEST/p05_DN+tlrc" \
MM06 "/Users/mafernan_admin/Desktop/anova_TEST/p06_DN+tlrc" \
MM07 "/Users/mafernan_admin/Desktop/anova_TEST/p07_DN+tlrc" \
MM08 "/Users/mafernan_admin/Desktop/anova_TEST/p08_DN+tlrc" \
MM09 "/Users/mafernan_admin/Desktop/anova_TEST/p09_DN+tlrc" \
MM10 "/Users/mafernan_admin/Desktop/anova_TEST/p10_DN+tlrc" \
MM11 "/Users/mafernan_admin/Desktop/anova_TEST/p11_DN+tlrc" \
MM14 "/Users/mafernan_admin/Desktop/anova_TEST/p14_DN+tlrc" \
MM15 "/Users/mafernan_admin/Desktop/anova_TEST/p15_DN+tlrc" \
MM16 "/Users/mafernan_admin/Desktop/anova_TEST/p16_DN+tlrc" \
MM17 "/Users/mafernan_admin/Desktop/anova_TEST/p17_DN+tlrc" \
MM18 "/Users/mafernan_admin/Desktop/anova_TEST/p18_DN+tlrc" \
MM19 "/Users/mafernan_admin/Desktop/anova_TEST/p19_DN+tlrc" \
MM20 "/Users/mafernan_admin/Desktop/anova_TEST/p20_DN+tlrc" \
MM21 "/Users/mafernan_admin/Desktop/anova_TEST/p21_DN+tlrc" \
MM101 "/Users/mafernan_admin/Desktop/anova_TEST/p101_DN+tlrc"



Edited 1 time(s). Last edit at 11/23/2022 07:49PM by BradyRoberts.