I added the "alpha" command line tools For ISAS_HN to my Matlab script. This works really well.
-I specify the ictal and interictal files
-Reorient if needed
then they automatically:
-create the TMAP
-I do a linear registration to the T1 (since they are coregistered to the interictal at this stage now)
-Then I threshold the TMAP to intenisities >=2 and/or >=4 (sort of a arbitrary guess for now- see below)
-Then they overlay and display on the T1 or any file other in my pipeline. Outstanding.
No user input or supervision other than specifying the files.

The question I have for you is this:
If I remember correctly from BIS legacy, in the help menu there was a t-distribution "table" showing the critical points of the t-distribution interchangeably as T-values, Z-scores, or P-values. I am speculating here that there were 14 normal SPECT pairs, and to interchange them this would suggest df=13? Then a 2 tailed t-test p=0.001 would need T-values >=4.2, and p=0.01 would need T-values >=3.0, p=0.05 would need T-values >2.2?
Is this reasonable?

I would like to correct this point in my pipeline.
It adds an important additional analysis tool to the presurgical evaluations and makes it extremely easy for users.