I am analyzing resting state data and usually use 3dttest++ with -Clustsim option to do a seed based group analysis. It looks like this option uses the input to 3dttest which is the final seed-based results obtained from 3dDeconvolve. I recently ran a 3 level 3dAnova and was a little confused about whether the stats are FDR corrected. The output from anova_bucket dataset shows significance (at least I think that is what the asterisks mean) :
– At sub-brick #0 ‘group_f:Inten’ datum type is short: 0 to 32767 [internal]
[* 1.48214e-05] 0 to 0.485652 [scaled]
– At sub-brick #1 ‘group_f:F-stat’ datum type is short: 0 to 1035 [internal]
[* 0.01] 0 to 10.35 [scaled]
statcode = fift; statpar = 2 26
– At sub-brick #2 ‘AI_m:Mean’ datum type is short: -5718 to 32767 [internal]
[* 2.33344e-05] -0.133426 to 0.764599 [scaled]
– At sub-brick #3 ‘AI_m:t-stat’ datum type is short: -5440 to 32700 [internal]
[* 0.001] -5.44 to 32.7 [scaled]

And when I open the dataset in the GUI, there is an associated q value (the p and q values change automatically depending on which sub-brick you have as overlay and threshold - when I look at t-test results, it’s only the q value that changes and the p value stays constant unless you manually change it - why is that?) but I wasn’t sure how to only show the clusters that are FDR corrected. I tried to run 3dClustSim and based on these threads, I thought the less processed file, as you stated here, should be used to determine acf values etc… But now I am confused because of how 3dttest++ runs it. Should I try to use the file generated immediately prior to regressing out wm and csf noise? or should the acf values come from a dataset that is not blurred?

Thanks for your help!

The *0.01 for sub-brick #1 say, shows the scaling of the
data on disk (shorts) to the real values (floats). It does
not related to FDR.

Did you apply a mask in the anova command? If not, the FDR
values will not be accurate. But otherwise, there is an
approximate p->q curve stored in the stats result, which the
GUI takes advantage of.

Regarding the t-test results, the p-value should change as
you change the threshold slider bar. Exactly which volumes
are you looking at?

  • rick