.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_01_plotting_plot_visualization.py>`     to download the full example code or to run this example in your browser via Binder
    .. rst-class:: sphx-glr-example-title

    .. _sphx_glr_auto_examples_01_plotting_plot_visualization.py:


NeuroImaging volumes visualization
==================================

Simple example to show Nifti data visualization.

Fetch data
----------


.. code-block:: default

    from nilearn import datasets

    # By default 2nd subject will be fetched
    haxby_dataset = datasets.fetch_haxby()

    # print basic information on the dataset
    print('First anatomical nifti image (3D) located is at: %s' %
          haxby_dataset.anat[0])
    print('First functional nifti image (4D) is located at: %s' %
          haxby_dataset.func[0])





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

 Out:

 .. code-block:: none

    First anatomical nifti image (3D) located is at: /home/varoquau/nilearn_data/haxby2001/subj2/anat.nii.gz
    First functional nifti image (4D) is located at: /home/varoquau/nilearn_data/haxby2001/subj2/bold.nii.gz




Visualization
-------------


.. code-block:: default

    from nilearn.image.image import mean_img

    # Compute the mean EPI: we do the mean along the axis 3, which is time
    func_filename = haxby_dataset.func[0]
    mean_haxby = mean_img(func_filename)

    from nilearn.plotting import plot_epi, show
    plot_epi(mean_haxby)




.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_visualization_001.png
    :alt: plot visualization
    :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none


    <nilearn.plotting.displays.OrthoSlicer object at 0x7f8bfc5f3940>



Extracting a brain mask
-----------------------
Simple computation of a mask from the fMRI data


.. code-block:: default

    from nilearn.masking import compute_epi_mask
    mask_img = compute_epi_mask(func_filename)

    # Visualize it as an ROI
    from nilearn.plotting import plot_roi
    plot_roi(mask_img, mean_haxby)




.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_visualization_002.png
    :alt: plot visualization
    :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none


    <nilearn.plotting.displays.OrthoSlicer object at 0x7f8bfc2f3bb0>



Applying the mask to extract the corresponding time series
----------------------------------------------------------


.. code-block:: default

    from nilearn.masking import apply_mask
    masked_data = apply_mask(func_filename, mask_img)

    # masked_data shape is (timepoints, voxels). We can plot the first 150
    # timepoints from two voxels

    # And now plot a few of these
    import matplotlib.pyplot as plt
    plt.figure(figsize=(7, 5))
    plt.plot(masked_data[:150, :2])
    plt.xlabel('Time [TRs]', fontsize=16)
    plt.ylabel('Intensity', fontsize=16)
    plt.xlim(0, 150)
    plt.subplots_adjust(bottom=.12, top=.95, right=.95, left=.12)

    show()



.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_visualization_003.png
    :alt: plot visualization
    :class: sphx-glr-single-img






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

   **Total running time of the script:** ( 0 minutes  23.863 seconds)


.. _sphx_glr_download_auto_examples_01_plotting_plot_visualization.py:


.. only :: html

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


  .. container:: binder-badge

    .. image:: https://mybinder.org/badge_logo.svg
      :target: https://mybinder.org/v2/gh/nilearn/nilearn.github.io/master?filepath=examples/auto_examples/01_plotting/plot_visualization.ipynb
      :width: 150 px


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

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



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

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


.. only:: html

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

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