The distinction between bath and myocardium is made w.r.t. the fiber lenght. Zero length fibers associate an element to the bath. As such, you need to assign fiber directions to the elements that should be part of the myocardium. Trivial fibers (i.e. (1,0,0) (0,1,0) for fibers and sheets respectively) can be assigned via "meshtool generate fibres" ..