Hi Chuck,
In your command line
AlphaSim –nx 161 –ny 191 –nz 151 –dx 3.125 –dy 3.125 –dz 6 –iter 1000 –rmm 15.1 –pthr 0.001 –out Output.txt
the dimensions of the image (161, 191, 151) and the voxel size of 3.125X3.125X6 are not consistent. To avoid the problem, you might consider creating a mask so that AlphaSim can obtain both the image dimensions and voxel size automatically from the mask file.
There is some controversial issue here. Doug Ward always recommends running multiple comparison correction with the original data parameters. However the group analysis is really done in tlrc space. So the correction might still be done in the tlrc space through the control of connectivity radius (option -rmm in AlphaSim).
Gang
