.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        Click :ref:`here <sphx_glr_download_auto_examples_01_plotting_plot_atlas.py>`     to download the full example code or to run this example in your browser via Binder
    .. rst-class:: sphx-glr-example-title

    .. _sphx_glr_auto_examples_01_plotting_plot_atlas.py:


Basic Atlas plotting
=======================

Plot the regions of a reference atlas (here the Harvard-Oxford atlas).

Retrieving the atlas data
-------------------------


.. code-block:: default


    from nilearn import datasets

    dataset = datasets.fetch_atlas_harvard_oxford('cort-maxprob-thr25-2mm')
    atlas_filename = dataset.maps

    print('Atlas ROIs are located at: %s' % atlas_filename)





.. rst-class:: sphx-glr-script-out

 Out:

 .. code-block:: none

    Atlas ROIs are located at: /home/varoquau/nilearn_data/fsl/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr25-2mm.nii.gz




Visualizing the Harvard-Oxford atlas
------------------------------------


.. code-block:: default


    from nilearn import plotting

    plotting.plot_roi(atlas_filename, title="Harvard Oxford atlas")




.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_atlas_001.png
    :alt: plot atlas
    :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 Out:

 .. code-block:: none


    <nilearn.plotting.displays.OrthoSlicer object at 0x7f8bfc69d5e0>



Visualizing the Harvard-Oxford atlas with contours
--------------------------------------------------


.. code-block:: default

    plotting.plot_roi(atlas_filename, view_type='contours',
                      title="Harvard Oxford atlas in contours")
    plotting.show()



.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_atlas_002.png
    :alt: plot atlas
    :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 Out:

 .. code-block:: none

    /home/varoquau/dev/nilearn/nilearn/plotting/displays.py:97: UserWarning: No contour levels were found within the data range.
      im = getattr(ax, type)(data_2d.copy(),





.. rst-class:: sphx-glr-timing

   **Total running time of the script:** ( 0 minutes  8.513 seconds)


.. _sphx_glr_download_auto_examples_01_plotting_plot_atlas.py:


.. only :: html

 .. container:: sphx-glr-footer
    :class: sphx-glr-footer-example


  .. container:: binder-badge

    .. image:: https://mybinder.org/badge_logo.svg
      :target: https://mybinder.org/v2/gh/nilearn/nilearn.github.io/master?filepath=examples/auto_examples/01_plotting/plot_atlas.ipynb
      :width: 150 px


  .. container:: sphx-glr-download sphx-glr-download-python

     :download:`Download Python source code: plot_atlas.py <plot_atlas.py>`



  .. container:: sphx-glr-download sphx-glr-download-jupyter

     :download:`Download Jupyter notebook: plot_atlas.ipynb <plot_atlas.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_