The issue was a bug in the drift correction to which resetting the centre of the input images is a sensible workaround. If you want, you can try the fix proposed in the population_template_space_init_drift_fix branch which should solve the FOV issue. Note that this fix does change the behaviour of population_template and is not yet part of the master code branch and it might change before it makes it there. To check the effect of the drift correction on the template shape, you could add the option -linear_no_drift_correction.