.. _sphx_glr_auto_examples_plot_evoked_data.py:


.. _tut_plot_evoked:

=====================
Visualize evoked data
=====================

Here we'll generate some attention for pecularities of visualizing the
HCP evoked outputs using MNE plotting functions.



.. code-block:: python

    # Author: Denis A. Enegemann
    # License: BSD 3 clause

    import os.path as op
    import hcp
    from hcp import preprocessing as preproc







we assume our data is inside a designated folder under $HOME



.. code-block:: python

    storage_dir = op.expanduser('~/mne-hcp-data')
    hcp_path = op.join(storage_dir, 'HCP')
    recordings_path = op.join(storage_dir, 'hcp-meg')
    subjects_dir = op.join(storage_dir, 'hcp-subjects')
    subject = '105923'  # our test subject
    data_type = 'task_working_memory'
    run_index = 0








Let's get the evoked data.



.. code-block:: python


    hcp_evokeds = hcp.read_evokeds(onset='stim', subject=subject,
                                   data_type=data_type, hcp_path=hcp_path)
    for evoked in hcp_evokeds:
        if not evoked.comment == 'Wrkmem_LM-TIM-face_BT-diff_MODE-mag':
            continue




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

 Out::

    Reading 4D PDF file /Users/dengemann/mne-hcp-data/HCP/105923/unprocessed/MEG/6-Wrkmem/4D/c,rfDC...
    Creating Neuromag info structure ...
    ... Setting channel info structure.
    ... no headshape file supplied, doing nothing.
    Currently direct inclusion of 4D weight tables is not supported. For critical use cases please take into account the MNE command "mne_create_comp_data" to include weights as printed out by the 4D "print_table" routine.


In order to plot topographic patterns we need to transform the sensor
positions to MNE coordinates one a copy of the data.
We're not using this these transformed data for any source analyses.
These take place in native BTI/4D coordinates.



.. code-block:: python


    evoked_viz = evoked.copy()
    preproc.map_ch_coords_to_mne(evoked_viz)
    evoked_viz.plot_joint()




.. image:: /auto_examples/images/sphx_glr_plot_evoked_data_001.png
    :align: center


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

 Out::

    Could not find layout for all the channels. Generating custom layout from channel positions.
    Failed to locate mag channel positions from layout. Inferring channel positions from data.


for subsequent analyses we would use `evoked` not `evoked_viz`.
See also :ref:`tut_compute_inverse_erf` to see how the story continues.


**Total running time of the script:** ( 0 minutes  4.500 seconds)



.. container:: sphx-glr-download

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



.. container:: sphx-glr-download

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

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

    `Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_