added input folder creation and checks for model/brains, model/xfms, model/objects, atlases/objects
added get.input options for getting model template class
changed Template class to accomodate for model objects and xfms
added register model-atlas stage, almost identical to other register functions
add stage info for stage_register_models, using stage_reg_atlas as guide
added model_reg_dir option which sets path of model to atlas registration, as these will be stored in a different location than the default output/registrations path
starting addition of image prep stage