Files input to 3dclustsim for thresholding mixed-effect models

Hello AFNI team!

I am using 3dlmer to model mixed effects (within-participant over time and between-participants). I was using the clustsim option on 3dttest++ command to get my cluster extent threshold for the results of this analysis.

I was unsure whether I should calculate the cluster extent threshold by inputting all the files that were input into the 3dlmer analysis even though some files are from the same subject and some are from different subjects. About 80% of the subjects have a scan at at least two timepoints and many have some at 3 timepoints. I wasn’t sure if the covairance between brain maps from the same subject would need to be addressed.

Thank you so much for your time and insight! :slight_smile: