.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/01_plotting/plot_atlas.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. 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 (Harvard-Oxford and Juelich atlases).

.. GENERATED FROM PYTHON SOURCE LINES 9-11

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

.. GENERATED FROM PYTHON SOURCE LINES 11-23

.. code-block:: default


    from nilearn import datasets

    dataset_ho = datasets.fetch_atlas_harvard_oxford('cort-maxprob-thr25-2mm')
    dataset_ju = datasets.fetch_atlas_juelich('maxprob-thr0-1mm')

    atlas_ho_filename = dataset_ho.filename
    atlas_ju_filename = dataset_ju.filename

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





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

 Out:

 .. code-block:: none

    Atlas ROIs are located at: /home/nicolas/nilearn_data/fsl/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr25-2mm.nii.gz
    Atlas ROIs are located at: /home/nicolas/nilearn_data/fsl/data/atlases/Juelich/Juelich-maxprob-thr0-1mm.nii.gz




.. GENERATED FROM PYTHON SOURCE LINES 24-26

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

.. GENERATED FROM PYTHON SOURCE LINES 26-31

.. code-block:: default


    from nilearn import plotting

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




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


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

 Out:

 .. code-block:: none


    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7fa52d39ab80>



.. GENERATED FROM PYTHON SOURCE LINES 32-34

Visualizing the Juelich atlas
------------------------------------

.. GENERATED FROM PYTHON SOURCE LINES 34-37

.. code-block:: default


    plotting.plot_roi(atlas_ju_filename, title="Juelich atlas")




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


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

 Out:

 .. code-block:: none


    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7fa52d2e1820>



.. GENERATED FROM PYTHON SOURCE LINES 38-40

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

.. GENERATED FROM PYTHON SOURCE LINES 40-44

.. code-block:: default

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




.. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_atlas_003.png
   :alt: plot atlas
   :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_atlas_003.png
   :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays/_axes.py:71: UserWarning: No contour levels were found within the data range.
      im = getattr(ax, type)(data_2d.copy(),




.. GENERATED FROM PYTHON SOURCE LINES 45-47

Visualizing the Juelich atlas with contours
--------------------------------------------------

.. GENERATED FROM PYTHON SOURCE LINES 47-50

.. code-block:: default

    plotting.plot_roi(atlas_ju_filename, view_type='contours',
                      title="Juelich atlas in contours")
    plotting.show()



.. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_atlas_004.png
   :alt: plot atlas
   :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_atlas_004.png
   :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays/_axes.py:71: 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  50.934 seconds)

**Estimated memory usage:**  138 MB


.. _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:: images/binder_badge_logo.svg
      :target: https://mybinder.org/v2/gh/nilearn/nilearn.github.io/main?filepath=examples/auto_examples/01_plotting/plot_atlas.ipynb
      :alt: Launch binder
      :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>`_