documentation suggests they can (says "imgs: 3D/4D Niimg-like object").
example:

from nilearn import datasets
from nilearn.input_data import NiftiMapsMasker, NiftiLabelsMasker


img = datasets.load_mni152_template()

atlas_img = datasets.fetch_atlas_destrieux_2009()["maps"]
labels_masker = NiftiLabelsMasker(atlas_img)

prob_atlas_img = datasets.fetch_atlas_harvard_oxford("cort-prob

Introduce a decode flag that produces a vertically flipped image, this would only be valid in non-progressive mode.