Which mask to use in 3dFWHMx to estimate smoothness?

AFNI Message Board
1

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

2

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