.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_segment_sphinx_macaque_ants_based.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_plot_segment_sphinx_macaque_ants_based.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_plot_segment_sphinx_macaque_ants_based.py:


.. _plot_segment_sphinx_macaque_ants_based:

==============================================================================
Plot the results of a segmentation with ANTS-based pipeline in sphinx position
==============================================================================

.. GENERATED FROM PYTHON SOURCE LINES 8-19

.. code-block:: Python


    # Authors: David Meunier, Bastien Cagna

    # License: BSD (3-clause)
    # sphinx_gallery_thumbnail_number = 2

    import os
    import os.path as op

    from macapype.utils.utils_tests import load_test_data








.. GENERATED FROM PYTHON SOURCE LINES 20-22

Testing plot in local
#############################################################################

.. GENERATED FROM PYTHON SOURCE LINES 22-25

.. code-block:: Python


    #orig_data_path = load_test_data("data_test_sphinx_macaque")








.. GENERATED FROM PYTHON SOURCE LINES 26-28

# Data preparation
##############################################################################

.. GENERATED FROM PYTHON SOURCE LINES 31-33

## Reorient
##==========================

.. GENERATED FROM PYTHON SOURCE LINES 33-49

.. code-block:: Python



    #orig_T1_file = op.join(orig_data_path, "sub-ziggy_T1w.nii")

    ## displaying results
    #orig_T1 = os.path.join(orig_data_path, "orig_T1.png")
    #cmd = "fsleyes render --outfile {} --size 1800 600 {}".format(orig_T1, orig_T1_file)
    #os.system(cmd)

    #import matplotlib.pyplot as plt  # noqa

    #fig, axs = plt.subplots(1, 1, figsize=(36, 24))
    #axs.imshow(plt.imread(orig_T1))
    #axs.axis('off')

    #plt.show()








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

   **Total running time of the script:** (0 minutes 0.002 seconds)


.. _sphx_glr_download_auto_examples_plot_segment_sphinx_macaque_ants_based.py:

.. only:: html

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

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

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

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

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

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_segment_sphinx_macaque_ants_based.zip <plot_segment_sphinx_macaque_ants_based.zip>`


.. only:: html

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

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