.. 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

        :ref:`Go to the end <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:: Python


    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(f"Atlas ROIs are located at: {atlas_ho_filename}")
    print(f"Atlas ROIs are located at: {atlas_ju_filename}")





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

 .. code-block:: none

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


    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

 .. code-block:: none


    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x733240c868d0>



.. GENERATED FROM PYTHON SOURCE LINES 32-34

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

.. GENERATED FROM PYTHON SOURCE LINES 34-37

.. code-block:: Python


    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

 .. code-block:: none


    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x73323daf0230>



.. GENERATED FROM PYTHON SOURCE LINES 38-40

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

.. GENERATED FROM PYTHON SOURCE LINES 40-47

.. code-block:: Python

    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

 .. code-block:: none

    /home/himanshu/.local/miniconda3/envs/nilearnpy/lib/python3.12/site-packages/nilearn/plotting/img_plotting.py:817: UserWarning: Data array used to create a new image contains 64-bit ints. This is likely due to creating the array with numpy and passing `int` as the `dtype`. Many tools such as FSL and SPM cannot deal with int64 in Nifti images, so for compatibility the data has been converted to int32.
      img = new_img_like(roi_img, data, affine=roi_img.affine)




.. GENERATED FROM PYTHON SOURCE LINES 48-50

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

.. GENERATED FROM PYTHON SOURCE LINES 50-55

.. code-block:: Python

    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-timing

   **Total running time of the script:** (1 minutes 4.171 seconds)

**Estimated memory usage:**  442 MB


.. _sphx_glr_download_auto_examples_01_plotting_plot_atlas.py:

.. only:: html

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

    .. container:: binder-badge

      .. image:: images/binder_badge_logo.svg
        :target: https://mybinder.org/v2/gh/nilearn/nilearn/main?urlpath=lab/tree/notebooks/auto_examples/01_plotting/plot_atlas.ipynb
        :alt: Launch binder
        :width: 150 px

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

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

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

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


.. only:: html

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

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