Hi Max,
After modifing the line as you suggested and running the following command:
population_template <odfs> out.mif -mask <masks> -type rigid -scratch regtest -nocleanup
I obtained the following template
Do you want to take a look to the linear_transforms_* folders? You can see the files here where the modified are the ones with the modified version of population_template (the password is template). Thanks in advance.
Best regards,
Manuel