"""
Visualizing a probabilistic atlas: the default mode in the MSDL atlas
=====================================================================

Visualizing a :term:`probabilistic atlas` requires visualizing the different
maps that compose it.

Here we represent the nodes constituting the default mode network in the
`MSDL atlas
<https://team.inria.fr/parietal/research/spatial_patterns/spatial-patterns-in-resting-state/>`_.

The tools that we need to leverage are:

* :func:`~nilearn.image.index_img` to retrieve the various maps composing
  the atlas

* Adding overlays on an existing brain display, to plot each of these maps

Alternatively, :func:`~nilearn.plotting.plot_prob_atlas` allows
to plot the maps in one step that
with less control over the plot (see below)

"""

# %%
# Fetching :term:`Probabilistic atlas` - MSDL atlas
# -------------------------------------------------
from nilearn import datasets

atlas_data = datasets.fetch_atlas_msdl()
atlas_filename = atlas_data.maps

# %%
# Visualizing a probabilistic atlas with plot_stat_map and add_overlay object
# ---------------------------------------------------------------------------
from nilearn import image, plotting

# First plot the map for the PCC: index 4 in the atlas
display = plotting.plot_stat_map(
    image.index_img(atlas_filename, 4),
    colorbar=False,
    title="DMN nodes in MSDL atlas",
    cmap="inferno",
)

# Now add as an overlay the maps for the ACC and the left and right
# parietal nodes
cmaps = [
    plotting.cm.black_blue,
    plotting.cm.black_green,
    plotting.cm.black_pink,
]
for index, cmap in zip([5, 6, 3], cmaps):
    display.add_overlay(image.index_img(atlas_filename, index), cmap=cmap)

plotting.show()


# %%
# Visualizing a :term:`probabilistic atlas` with ``plot_prob_atlas``
# ------------------------------------------------------------------
#
# Alternatively, we can create a new 4D-image by selecting
# the 3rd, 4th, 5th and 6th (zero-based) probabilistic map from atlas
# via :func:`~nilearn.image.index_img`
# and use :func:`~nilearn.plotting.plot_prob_atlas` (added in version 0.2)
# to plot the selected nodes in one step.
#
# Unlike :func:`~nilearn.plotting.plot_stat_map` this works with 4D images

dmn_nodes = image.index_img(atlas_filename, [3, 4, 5, 6])
# Note that dmn_node is now a 4D image
print(dmn_nodes.shape)

# %%
display = plotting.plot_prob_atlas(
    dmn_nodes, cut_coords=(0, -55, 29), title="DMN nodes in MSDL atlas"
)
plotting.show()

# sphinx_gallery_dummy_images=2
