The mask should be whatever the mask is for your actual analysis.
If you are looking at results within a different mask than you used for the 3dClustSim command, then the cluster sizes are not valid. If you are only looking at results within gray matter, then you can certainly use that as a mask (for both your analysis and your 3dClustSim command).
-Mike
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From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Mike [[log in to unmask]]
Sent: Saturday, January 16, 2016 2:08 PM
To: [log in to unmask]
Subject: Re: [SPM] 3dClustSim further question
Dear Donald,
Thanks for your opinion. I just notice that, in most fMRI papers using 3dClustSim, how reseachers determine the mask for Monte Carlo simulations is not described (e.g., only "As estimated using 3dClustSim, this cluster extent threshold gave rise to a corrected whole brain cluster-wise significance level of p < 0.05". Nothing else.). Today I can determine an average gray matter mask of my group and trhesholded it at 0.2, but next time I can threshold it at 0.5.....!?
Mike
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