3dClustSim

AFNI Message Board
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Dear AFNI experts,

I am trying to estimate cluster thresholds for my analyses with 3dClustSim. Because I have done preprocessing and first level analyses in SPM, I’m a bit puzzled by what to include in the 3dFWHMx and 3dClustSim commands. After carefully reading the helps and the message board, the following steps are what I have come up with. I’m still a bit unsure as to what mask-files to use at what step. Would you be so kind as to check whether this approach sounds okay?

  1. I took the square root of the ResMS.nii files (which are first-level output) per subject

  2. I ran per subject: 3dFWHMx -mask -mask.nii -acf >> acf.txt
    Here I used the individual mask-files created on first level, is this correct? Or do I use the same (group-level, created on second level) mask for all the subjects?

  3. I calculated the mean acf-value over all the subjects

  4. I ran: 3dClustSim -mask mask.nii -acf [the 3 mean acf values] >> thresholds.txt
    Here I used the group level (created on second level) mask, would that be correct? I also tried running this with -nxyz and -dxyz specified, but then the output was very different, so I’m a bit unsure about this.

Thank you!
Kind regards, Rozemarijn