.. 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).

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


.. 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: <class 'nibabel.nifti1.Nifti1Image'>
    data shape (91, 109, 91)
    affine: 
    [[   2.    0.    0.  -90.]
     [   0.    2.    0. -126.]
     [   0.    0.    2.  -72.]
     [   0.    0.    0.    1.]]
    metadata:
    <class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
    sizeof_hdr      : 348
    data_type       : b''
    db_name         : b''
    extents         : 0
    session_error   : 0
    regular         : b''
    dim_info        : 0
    dim             : [  3  91 109  91   1   1   1   1]
    intent_p1       : 0.0
    intent_p2       : 0.0
    intent_p3       : 0.0
    intent_code     : none
    datatype        : uint8
    bitpix          : 8
    slice_start     : 0
    pixdim          : [1. 2. 2. 2. 1. 1. 1. 1.]
    vox_offset      : 0.0
    scl_slope       : nan
    scl_inter       : nan
    slice_end       : 0
    slice_code      : unknown
    xyzt_units      : 0
    cal_max         : 0.0
    cal_min         : 0.0
    slice_duration  : 0.0
    toffset         : 0.0
    glmax           : 0
    glmin           : 0
    descrip         : b''
    aux_file        : b''
    qform_code      : unknown
    sform_code      : aligned
    quatern_b       : 0.0
    quatern_c       : 0.0
    quatern_d       : 0.0
    qoffset_x       : -90.0
    qoffset_y       : -126.0
    qoffset_z       : -72.0
    srow_x          : [  2.   0.   0. -90.]
    srow_y          : [   0.    2.    0. -126.]
    srow_z          : [  0.   0.   2. -72.]
    intent_name     : b''
    magic           : b'n+1'
    Atlas ROIs are located at: <class 'nibabel.nifti1.Nifti1Image'>
    data shape (182, 218, 182)
    affine: 
    [[   1.    0.    0.  -91.]
     [   0.    1.    0. -126.]
     [   0.    0.    1.  -72.]
     [   0.    0.    0.    1.]]
    metadata:
    <class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
    sizeof_hdr      : 348
    data_type       : b''
    db_name         : b''
    extents         : 0
    session_error   : 0
    regular         : b''
    dim_info        : 0
    dim             : [  3 182 218 182   1   1   1   1]
    intent_p1       : 0.0
    intent_p2       : 0.0
    intent_p3       : 0.0
    intent_code     : none
    datatype        : uint8
    bitpix          : 8
    slice_start     : 0
    pixdim          : [1. 1. 1. 1. 1. 1. 1. 1.]
    vox_offset      : 0.0
    scl_slope       : nan
    scl_inter       : nan
    slice_end       : 0
    slice_code      : unknown
    xyzt_units      : 0
    cal_max         : 0.0
    cal_min         : 0.0
    slice_duration  : 0.0
    toffset         : 0.0
    glmax           : 0
    glmin           : 0
    descrip         : b''
    aux_file        : b''
    qform_code      : unknown
    sform_code      : aligned
    quatern_b       : 0.0
    quatern_c       : 0.0
    quatern_d       : 0.0
    qoffset_x       : -91.0
    qoffset_y       : -126.0
    qoffset_z       : -72.0
    srow_x          : [  1.   0.   0. -91.]
    srow_y          : [   0.    1.    0. -126.]
    srow_z          : [  0.   0.   1. -72.]
    intent_name     : b''
    magic           : b'n+1'




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


.. code-block:: default


    from nilearn import plotting

    plotting.plot_roi(atlas_ho_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 0x7fc02c265d00>



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


.. code-block:: default


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




.. 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


    <nilearn.plotting.displays.OrthoSlicer object at 0x7fc02a01cf40>



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


.. code-block:: default

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




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


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

 Out:

 .. code-block:: none

    /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays.py:101: UserWarning: No contour levels were found within the data range.
      im = getattr(ax, type)(data_2d.copy(),




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


.. code-block:: default

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



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


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

 Out:

 .. code-block:: none

    /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays.py:101: 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  47.637 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:: 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>`_