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

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

.. _sphx_glr_auto_examples_volume_surface_rendering_plot_volumetric_mask_as_surface.py:


================
Rendering volumetric masks as surfaces
================

This is a quick demo showing how to plot a surface mesh generated from a volumetric mask.

Here, we use the template MNI152 T1-weighted brain to create an arbitrary mask. 


First, let's load the basic required libraries

.. GENERATED FROM PYTHON SOURCE LINES 13-17

.. code-block:: default

    import matplotlib.pyplot as plt
    from cerebro import cerebro_brain_utils as cbu
    from cerebro import cerebro_brain_viewer as cbv








.. GENERATED FROM PYTHON SOURCE LINES 18-20

Plotting a surface from volumetric masks
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. GENERATED FROM PYTHON SOURCE LINES 20-45

.. code-block:: default


    # Define a viewer
    cerebro_viewer = cbv.Cerebro_brain_viewer(offscreen=True, background_color=(1,1,1,1))

    # Load an example volumetric file
    nii_file = cbu.get_data_file(f"templates/MNI152/MNI152_T1_2mm_brain.nii.gz")

    # Create a 3D surface of the mask
    volumetric_mask = cerebro_viewer.visualize_mask_surface(
        nii_file,  # The volumetric file
        6000,  # An arbitrary threshold to mask the data
        color=(0.9, 0.4, 0.5, 1),  # Let's make the brain look pink!
        gradient_direction="ascent",  # This defines the surface normal directions
        smoothing=400  # Iteratively smooth the surface to look better
    )


    fig, ax = plt.subplots(figsize=(8,7))
    plt.subplots_adjust(wspace=0, hspace=0)
    ax.axis('off')
    cerebro_viewer.offscreen_draw_to_matplotlib_axes(ax)

    # Clear this viewer
    cerebro_viewer.viewer.window.destroy()
    plt.show()



.. image-sg:: /auto_examples/volume_surface_rendering/images/sphx_glr_plot_volumetric_mask_as_surface_001.png
   :alt: plot volumetric mask as surface
   :srcset: /auto_examples/volume_surface_rendering/images/sphx_glr_plot_volumetric_mask_as_surface_001.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** ( 0 minutes  10.731 seconds)


.. _sphx_glr_download_auto_examples_volume_surface_rendering_plot_volumetric_mask_as_surface.py:

.. only:: html

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




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

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

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

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


.. only:: html

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

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