Hi all,

I'm looking into the power analysis option for AlphaSim and I'm having some trouble understanding the input parameters.
I've read the readme doc and it does have an example but it didn't say how the parameters were derived.

Specifically,
1. How do you define the active region?
2. How do you calculate the Z score separation between signal and noise?

We tried tackling the problem ourselves but the results seems puzzling. For the Z score separation we took the contrast map generated by SPM and transformed it into Z score space, and then extracted values for voxels inside the ROI (signal) and outside the ROI but still within the brain (noise). Finally, we took the mean of each and subtracted. For the active region we tried a number of things, including the size of the ROI (we came up with number for the 3 dimensions so the volume matched), the dimensions of the whole image, and a 10x10x10 volume just to see what we're dealing with.
We found that:
A. The simulation cuts off at cluster size 9999, so having an active region that's too big (i.e. whole image) is probably not the right thing to do.
B. Power decreases with increasing cluster size, which is somewhat counter intuitive.
C. When we used the Z score we calculated only the cluster very close to the maximum had frequency counts greater than 0

We concluded that we probably aren't using this right so any pointers on this will be greatly appreciated.

PS. why is the active region not defined by a volume? Does the shape of the region matter?