:orphan:

.. _tutorial_examples:

Tutorials: getting started with the pyAFQ Python library
=========================================================

These tutorials provide a walk-through of basic pyAFQ usage and some more
advanced use-cases. Each one of these pages contains code that users can run
from top to bottom. The code will download the data necessary to run the
tutorial, and will save results as it goes along.


.. toctree::
    :maxdepth: 2


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    <div class="sphx-glr-thumbnails">

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    <div class="sphx-glr-thumbcontainer" tooltip="There are two ways to use pyAFQ &lt;/howto/getting_started&gt;: through the command line interface, and by writing Python code. This tutorial will walk you through the basics of the latter, using pyAFQ&#x27;s Python Application Programming Interface (API).">

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  .. image:: /tutorials/tutorial_examples/images/thumb/sphx_glr_plot_001_afq_api_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_tutorial_examples_plot_001_afq_api.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Getting started programming with pyAFQ</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The pyAFQ API relies heavily on the Brain Imaging Data Standard (BIDS), a widely used standard for organizing and describing neuroimaging data. This means that the software assumes that its inputs are organized according to the BIDS specification and its outputs conform where possible with BIDS.">

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  .. image:: /tutorials/tutorial_examples/images/thumb/sphx_glr_plot_002_bids_layout_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_tutorial_examples_plot_002_bids_layout.py`

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      <div class="sphx-glr-thumbnail-title">How pyAFQ uses BIDS</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Visualizing the results of a pyAFQ analysis is useful because it allows us to inspect the results of the analysis and to communicate the results to others. The pyAFQ pipeline produces a number of different kinds of outputs, including visualizations that can be used for quality control and for quick examination of the results of the analysis.">

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  .. image:: /tutorials/tutorial_examples/images/thumb/sphx_glr_plot_003_viz_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_tutorial_examples_plot_003_viz.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Visualizing AFQ derivatives</div>
    </div>


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    </div>


.. toctree::
   :hidden:

   /tutorials/tutorial_examples/plot_001_afq_api
   /tutorials/tutorial_examples/plot_002_bids_layout
   /tutorials/tutorial_examples/plot_003_viz


.. only:: html

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

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

      :download:`Download all examples in Python source code: tutorial_examples_python.zip </tutorials/tutorial_examples/tutorial_examples_python.zip>`

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

      :download:`Download all examples in Jupyter notebooks: tutorial_examples_jupyter.zip </tutorials/tutorial_examples/tutorial_examples_jupyter.zip>`


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

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