.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/run_run_gmd_mean.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_run_run_gmd_mean.py>`
        to download the full example code.

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

.. _sphx_glr_auto_examples_run_run_gmd_mean.py:


UKB VBM GMD Extraction
======================

Authors: Federico Raimondo

License: BSD 3 clause

.. GENERATED FROM PYTHON SOURCE LINES 9-54




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

 .. code-block:: none


    Added README.md to /github/home/nilearn_data


    Dataset created in /github/home/nilearn_data/oasis1

    Downloading data from https://www.nitrc.org/frs/download.php/6364/archive_dartel.tgz ...

    Downloaded 122421248 of 905208634 bytes (13.5%,    6.4s remaining)
    Downloaded 263708672 of 905208634 bytes (29.1%,    4.9s remaining)
    Downloaded 410992640 of 905208634 bytes (45.4%,    3.6s remaining)
    Downloaded 560570368 of 905208634 bytes (61.9%,    2.5s remaining)
    Downloaded 710836224 of 905208634 bytes (78.5%,    1.4s remaining)
    Downloaded 860422144 of 905208634 bytes (95.1%,    0.3s remaining) ...done. (7 seconds, 0 min)
    Extracting data from /github/home/nilearn_data/oasis1/7088b0bf88f5650db26e32ec3afdd589/archive_dartel.tgz..... done.
    Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152Lin/tpl-MNI152Lin_res-01_T1w.nii.gz

      0%|          | 0.00/10.7M [00:00<?, ?B/s]
      7%|▋         | 718k/10.7M [00:00<00:01, 7.17MB/s]
     76%|███████▌  | 8.08M/10.7M [00:00<00:00, 46.2MB/s]
    100%|██████████| 10.7M/10.7M [00:00<00:00, 47.3MB/s]






|

.. code-block:: Python

    import tempfile

    import junifer.testing.registry  # noqa: F401
    from junifer.api import run


    datagrabber = {
        "kind": "OasisVBMTestingDataGrabber",
    }

    markers = [
        {
            "name": "Schaefer1000x7_TrimMean80",
            "kind": "ParcelAggregation",
            "parcellation": "Schaefer1000x7",
            "method": "trim_mean",
            "method_params": {"proportiontocut": 0.2},
        },
        {
            "name": "Schaefer1000x7_Mean",
            "kind": "ParcelAggregation",
            "parcellation": "Schaefer1000x7",
            "method": "mean",
        },
        {
            "name": "Schaefer1000x7_Std",
            "kind": "ParcelAggregation",
            "parcellation": "Schaefer1000x7",
            "method": "std",
        },
    ]

    storage = {
        "kind": "SQLiteFeatureStorage",
    }

    with tempfile.TemporaryDirectory() as tmpdir:
        uri = f"{tmpdir}/test.sqlite"
        storage["uri"] = uri
        run(
            workdir="/tmp",
            datagrabber=datagrabber,
            markers=markers,
            storage=storage,
        )


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

   **Total running time of the script:** (35 minutes 36.024 seconds)


.. _sphx_glr_download_auto_examples_run_run_gmd_mean.py:

.. only:: html

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

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

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

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

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

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: run_run_gmd_mean.zip <run_run_gmd_mean.zip>`


.. only:: html

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

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