Which mask to use in 3dFWHMx to estimate smoothness?

Dear experts,

I just starts learning AlphaSim, and have a question on the choice of a mask for smoothness estimation in 3dFWHMx.

My study is to use voxel-based GM measure to perform statistical analysis. So the mask in statistical analysis was a GM mask.

However, when I use 3dFWHMx to estimate smoothness for running 3dClustersim later on, I am confused on how to choose the right mask. Should I use the whole brain mask, or should I use the GM mask to estimate smoothness?

Many thanks!

Haobo Zhang

It does make sense to use the gray matter mask when estimating the ACF (Auto Correlation Function) in your case.