Hi Mahsa,
> Is alphasim a command or a toolbox in afni?
AlphaSim is outdated. Use 3dClustSIm, which is a command-line program. Type
3dClustSim -help
for its usage and examples.
> How could I threshold my resulted image using alphasim(p<0.05) and save them as images?
Once you find out the minimum cluster size in terms of number of voxels from 3dClustSim, click the Clusterize button (next to the colorbar at the top) on the 'afni' GUI controller, and set Voxels with that minimum cluster size. After that, click Rpt button underneath, and you should be able to obtain a cluster list table.
Gang