:orphan:



.. _sphx_glr_auto_examples:



.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_workflows:

Tutorials
---------

The following tutorials contain the workflow and code to simulate and visualize commonly
studied M/EEG signals including event related potentials and low frequency rhythms in the
alpha, beta and gamma bands. The tutorial workflows, and all parameter values used,
are based on the detailed tutorials provided on the `HNN GUI website
<https://hnn.brown.edu/tutorials>`_, and reproduce a subset of examples and figures in the
more elaborated GUI tutorials using the HNN-core API.

We strongly recommend that you
first go through the background information provided on the `HNN website
<https://hnn.brown.edu/overview-uniqueness/>`_ and each of the HNN GUI tutorials,
after which the code and instructions in these HNN-core tutorials will be clearer.
All tutorials build from our prior publications investigating the origin of ERPs and
brain rhythms in the somatosensory system, and parameter and data sets are provided to
help users get started.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate a threshold level tactile evoked response, as detaile...">

.. only:: html

 .. figure:: /auto_examples/workflows/images/thumb/sphx_glr_plot_simulate_evoked_thumb.png
     :alt: 01. Simulate Event Related Potentials (ERPs)

     :ref:`sphx_glr_auto_examples_workflows_plot_simulate_evoked.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/workflows/plot_simulate_evoked

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate alpha and beta frequency activity in the alpha/beta c...">

.. only:: html

 .. figure:: /auto_examples/workflows/images/thumb/sphx_glr_plot_simulate_alpha_thumb.png
     :alt: 02. Simulate Alpha and Beta Rhythms

     :ref:`sphx_glr_auto_examples_workflows_plot_simulate_alpha.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/workflows/plot_simulate_alpha

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate gamma rhythms via the well established pyramidal-inte...">

.. only:: html

 .. figure:: /auto_examples/workflows/images/thumb/sphx_glr_plot_simulate_gamma_thumb.png
     :alt: 03. Simulate Gamma Rhythms

     :ref:`sphx_glr_auto_examples_workflows_plot_simulate_gamma.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/workflows/plot_simulate_gamma

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to calculate an inverse solution of the median nerve evoked respo...">

.. only:: html

 .. figure:: /auto_examples/workflows/images/thumb/sphx_glr_plot_simulate_somato_thumb.png
     :alt: 04. From MEG sensor-space data to HNN simulation

     :ref:`sphx_glr_auto_examples_workflows_plot_simulate_somato.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/workflows/plot_simulate_somato

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how event related potentials (ERP) are modulated by prestimulus beta ...">

.. only:: html

 .. figure:: /auto_examples/workflows/images/thumb/sphx_glr_plot_simulate_beta_thumb.png
     :alt: 05. Simulate beta modulated ERP

     :ref:`sphx_glr_auto_examples_workflows_plot_simulate_beta.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/workflows/plot_simulate_beta
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_howto:

How to
------

These are short examples that show how to use HNN-core API to accomplish specific
tasks.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to inspect the firing pattern of cells in the HNN model.">

.. only:: html

 .. figure:: /auto_examples/howto/images/thumb/sphx_glr_plot_firing_pattern_thumb.png
     :alt: 01. Plot firing pattern

     :ref:`sphx_glr_auto_examples_howto_plot_firing_pattern.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/howto/plot_firing_pattern

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The main output of HNN simulations is the &#x27;dipole&#x27; waveform, i.e., the net intracellular curren...">

.. only:: html

 .. figure:: /auto_examples/howto/images/thumb/sphx_glr_plot_record_extracellular_potentials_thumb.png
     :alt: 02. Record extracellular potentials

     :ref:`sphx_glr_auto_examples_howto_plot_record_extracellular_potentials.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/howto/plot_record_extracellular_potentials

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to modify the network connectivity.">

.. only:: html

 .. figure:: /auto_examples/howto/images/thumb/sphx_glr_plot_connectivity_thumb.png
     :alt: 03. Modifying local connectivity

     :ref:`sphx_glr_auto_examples_howto_plot_connectivity.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/howto/plot_connectivity

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use the MPI backend for simulating dipoles using HNN-core.">

.. only:: html

 .. figure:: /auto_examples/howto/images/thumb/sphx_glr_plot_simulate_mpi_backend_thumb.png
     :alt: 04. Use MPI backend for parallelization

     :ref:`sphx_glr_auto_examples_howto_plot_simulate_mpi_backend.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/howto/plot_simulate_mpi_backend

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to optimize the parameters of the model simulation to match an ex...">

.. only:: html

 .. figure:: /auto_examples/howto/images/thumb/sphx_glr_plot_optimize_evoked_thumb.png
     :alt: 05. Optimize simulated evoked response parameters

     :ref:`sphx_glr_auto_examples_howto_plot_optimize_evoked.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/howto/plot_optimize_evoked
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. only :: html

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


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

    :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`



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

    :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


.. only:: html

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

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