.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/norun_hcpfc_pearson.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_auto_examples_norun_hcpfc_pearson.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_norun_hcpfc_pearson.py:


HCP FC Extraction
======================

Authors: Leonard Sasse
License: BSD 3 clause

.. GENERATED FROM PYTHON SOURCE LINES 8-82

.. code-block:: Python



    from junifer.api import run


    datagrabber = {
        "kind": "HCPOpenAccess",
        "modality": "fMRI",
        "preprocessed": "ICA+FIX",
        "space": "volumetric",
    }

    custom_confound_strategy = {
        "filter": "butterworth",
        "detrend": True,
        "high_pass": 0.01,
        "low_pass": 0.08,
        "standardize": True,
        "confounds": ["csf", "wm", "gsr"],
        "derivatives": True,
        "squares": True,
        "other": [],
    }

    markers = [
        {
            "name": "Power264_FCPearson",
            "kind": "FunctionalConnectivity",
            "parcellation": "Power264",
            "method": "Pearson",
            "confound_strategy": "Params36",
        },
        {
            "name": "Schaefer400x17_FCPearson",
            "kind": "FunctionalConnectivity",
            "parcellation": "Schaefer400x17",
            "method": "Pearson",
            "confound_strategy": "Params24",
        },
        {
            "name": "Power264_FCSpearman",
            "kind": "FunctionalConnectivity",
            "parcellation": "Power264",
            "method": "Spearman",
            "confound_strategy": "ICAAROMA",
        },
        {
            "name": "Schaefer400x17_FCSpearman",
            "kind": "FunctionalConnectivity",
            "parcellation": "Schaefer400x17",
            "method": "Spearman",
            "confound_strategy": "path/to/predefined/confound_file.tsv",
        },
        {
            "name": "Schaefer400x17_FCSpearman",
            "kind": "FunctionalConnectivity",
            "parcellation": "Schaefer400x17",
            "method": "Spearman",
            "confound_strategy": custom_confound_strategy,
        },
    ]

    storage = {
        "kind": "SQLiteFeatureStorage",
        "uri": "/data/project/juniferexample",
    }

    run(
        workdir="/tmp",
        datagrabber=datagrabber,
        elements=[("100408", "REST1", "LR")],
        markers=markers,
        storage=storage,
    )


.. _sphx_glr_download_auto_examples_norun_hcpfc_pearson.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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