:orphan:

.. _howto_examples:

How to examples
================

These examples provide details of various advanced and more complex usage
of pyAFQ. These are intended to provide a reference and answer questions
about the variety of pyAFQ functionality that is available.

.. toctree::
    :maxdepth: 2


.. raw:: html

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


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="pyAFQ is designed to be customizable and extensible. This example shows how you can customize i...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_add_custom_bundle_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_add_custom_bundle.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">How to add new bundles into pyAFQ (SLF 1/2/3 Example)</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The following is an example of tractometry for infant bundles. This example and resulting pyAFQ...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_baby_afq_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_baby_afq.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">BabyAFQ : tractometry for infant dMRI data</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The cerebellar peduncles are white matter tracts that connect the cerebellum to the brainstem a...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_cerebellar_peduncles_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_cerebellar_peduncles.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Delineating cerebellar peduncles</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="To analyze these datasets, large amounts of compute are needed. One way to gain access to massi...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_cloudknot_example_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_cloudknot_example.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Using cloudknot to run pyAFQ on AWS batch:</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="AFQ with HCP data">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_cloudknot_hcp_example_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_cloudknot_hcp_example.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">AFQ with HCP data</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="pyAFQ is designed to be customizable and extensible. This example shows how you can customize i...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_plot_acoustic_radiations_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_plot_acoustic_radiations.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">How to add new bundles into pyAFQ (Acoustic Radiations Example)</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Callosal bundles using AFQ API">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_plot_afq_callosal_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_plot_afq_callosal.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Callosal bundles using AFQ API</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The free-water DTI model [1, 2]_ fits a two compartment model to dMRI data with more than one n...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_plot_afq_fwdti_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_plot_afq_fwdti.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">How to use Free water DTI</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="pyAFQ is designed to be customizable and extensible. This example shows how you can customize i...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_plot_optic_radiations_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_plot_optic_radiations.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">How to add new bundles into pyAFQ(Optic Radiations Example)</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="For bundle recognition, pyAFQ defaults to use the waypoint ROI approach described in [Yeatman20...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_plot_recobundles_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_plot_recobundles.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Using RecoBundles for bundle recognition</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Two-dimensional figures of anatomical data are somewhat limited, because of the complex three-d...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_plot_stages_of_tractometry_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_plot_stages_of_tractometry.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Making videos the different stages of tractometry</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="An example using the AFQ API to find bundles as defined by endpoint ROIs from freesurfer. This ...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_use_subject_space_rois_from_freesurfer_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_use_subject_space_rois_from_freesurfer.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Using Subject Space ROIs from Freesurfer</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The pyAFQ software can be configured to find all of its default set of white matter pathways, o...">

.. only:: html

  .. image:: /howto/howto_examples/images/thumb/sphx_glr_vof_example_thumb.png
    :alt:

  :ref:`sphx_glr_howto_howto_examples_vof_example.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">How to segment out only some bundles</div>
    </div>


.. raw:: html

    </div>


.. toctree::
   :hidden:

   /howto/howto_examples/add_custom_bundle
   /howto/howto_examples/baby_afq
   /howto/howto_examples/cerebellar_peduncles
   /howto/howto_examples/cloudknot_example
   /howto/howto_examples/cloudknot_hcp_example
   /howto/howto_examples/plot_acoustic_radiations
   /howto/howto_examples/plot_afq_callosal
   /howto/howto_examples/plot_afq_fwdti
   /howto/howto_examples/plot_optic_radiations
   /howto/howto_examples/plot_recobundles
   /howto/howto_examples/plot_stages_of_tractometry
   /howto/howto_examples/use_subject_space_rois_from_freesurfer
   /howto/howto_examples/vof_example


.. 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: howto_examples_python.zip </howto/howto_examples/howto_examples_python.zip>`

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

      :download:`Download all examples in Jupyter notebooks: howto_examples_jupyter.zip </howto/howto_examples/howto_examples_jupyter.zip>`


.. only:: html

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

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