To back up a moment, the purpose of gen_group_command.py is to help write the script for 3dttest++ for example, while allowing one to use wildcards to select subject datasets. It has a similar functionality to that of uber_ttest.py, except that it does not have a graphical interface.

Typically, you should not edit it resulting command script (in this case, the script that runs 3dttest++).
We can fix the problems with the 3dttest++ script (the data_dir has been altered, and there is a wildcard character in it), but it is the gen_group_command.py script that should really be fixed, and then it will create the 3dttest++ command script, which you should try not to edit.

The way you are running the 3dttest++ script is good, you can even run the gen_group_command.py script that way. But let's now back up and fix the ggc one.

The gen_group_command.py script seemed okay, except that it selected datasets using:

-dsets $dirA/s01/s01.results/pACC.z+tlrc*HEAD \

But that will not list all datasets, because they are not all in the s01 directory. Try something like:

-dsets $dirA/s*/s*.results/pACC.z+tlrc*HEAD \

- rick