Meng,

> Could anyone explain why I must use the original
> data with acquired resolusion?

Some people do suggest running Monte Carlo simulations in the EPI resolution, but I feel that you should be OK with any resolution if you appropriately set up the connecitivity raidus in AlphaSim (option -rmm) so that the original resolution is considered in terms of cluster formation. And with your interpolated resolution, you don't have to worry about your mask.

> The acquired resolusion of my data is
> 3.75mm*3.75mm*5mm, (5 mm thickness, and 2
> mm gap). What should I use in AlphaSim?
> 3.75*3.75*5 or 3.75*3.75*7?

Connectivity radius is a little arbitrary depending how you consider a cluster is formed. Just give two extreme scenarios in your case: you can set it up with 3.8 mm (slightly longer than the shortest dimension of your voxel size 3.75*3.75*5) if you want to be a little conservative, or 8.8 mm (slightly longer than the diagonal of voxel size 3.75*3.75*7) if you want to be very generous.

Gang