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

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        Click :ref:`here <sphx_glr_download_auto_examples_quickflat_plot_dropout.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_quickflat_plot_dropout.py:


===================================
Plot dropout regions on the flatmap
===================================

A dropout region is a region with very low EPI signal. In pycortex a
crosshatch is used to display such dropout regions.

The crosshatches are created using the reference nifti image file
with a threshold.
Setting the `with_dropout=True` parameter in `quickflat.make_figure`
takes the reference nifti image file and computes a thresholded version
of this using the following formula:

    FIXME:
    .. code-block:: python
        rawdata[rawdata==0] = np.mean(rawdata[rawdata!=0])
        normdata = (rawdata - rawdata.min()) / (rawdata.max() - rawdata.min())
        normdata = (1 - normdata) ** power

.. GENERATED FROM PYTHON SOURCE LINES 21-34



.. image-sg:: /auto_examples/quickflat/images/sphx_glr_plot_dropout_001.png
   :alt: plot dropout
   :srcset: /auto_examples/quickflat/images/sphx_glr_plot_dropout_001.png
   :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    Failed to get connection
    ** (inkscape:5219): CRITICAL **: 01:27:52.316: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
    ** (inkscape:5219): CRITICAL **: 01:27:52.317: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
    ** (inkscape:5219): CRITICAL **: 01:27:52.317: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed






|

.. code-block:: default


    import cortex
    import numpy as np
    np.random.seed(1234)

    # Create a random pycortex Volume
    volume = cortex.Volume.random(subject='S1', xfmname='fullhead')

    # Plot a flatmap with the data projected onto the surface
    # Highlight the curvature and dropout regions
    _ = cortex.quickflat.make_figure(volume,
                                     with_curvature=True,
                                     with_dropout=True)


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

   **Total running time of the script:** ( 0 minutes  3.200 seconds)


.. _sphx_glr_download_auto_examples_quickflat_plot_dropout.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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