.. _examples-index:

Gallery of Examples
===================




.. warning::

    If you want to run the examples, make sure you execute them in a directory
    where you have write permissions, or you copy the examples into such a
    directory. If you install nilearn manually, make sure you have followed
    :ref:`the instructions <installation>`.

.. note::

    A few examples may not run with scikit-learn versions older than
    0.14.1.

General examples
----------------

General-purpose and introductory examples for nilearn.




.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="A simple example of basic Python numerics and how to plot it. ">

.. figure:: ./images/thumb/plot_python_101.png
    :target: ./plot_python_101.html

    :ref:`example_plot_python_101.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   ./plot_python_101


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="A simple example showing how to load an existing Nifti file and use basic nilearn functionaliti...">

.. figure:: ./images/thumb/plot_nilearn_101.png
    :target: ./plot_nilearn_101.html

    :ref:`example_plot_nilearn_101.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   ./plot_nilearn_101


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="Here is a simple example of automatic mask computation using the nifti masker. The mask is comp...">

.. figure:: ./images/thumb/plot_nifti_simple.png
    :target: ./plot_nifti_simple.html

    :ref:`example_plot_nifti_simple.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   ./plot_nifti_simple


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="This example shows how to use the Localizer dataset in a basic analysis. A standard Anova is pe...">

.. figure:: ./images/thumb/plot_localizer_simple_analysis.png
    :target: ./plot_localizer_simple_analysis.html

    :ref:`example_plot_localizer_simple_analysis.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   ./plot_localizer_simple_analysis


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="Here is a simple example of decoding, reproducing the Haxby 2001 study on a face vs cat discrim...">

.. figure:: ./images/thumb/plot_haxby_simple.png
    :target: ./plot_haxby_simple.html

    :ref:`example_plot_haxby_simple.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   ./plot_haxby_simple


.. raw:: html

    <div style='clear:both'></div>
    


Functional connectivity
-----------------------

See :ref:`parcellating_brain`, :ref:`extracting_rsn` or
:ref:`functional_connectomes` for more details.




.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="An example applying CanICA to resting-state data. This example applies it to 40 subjects of the...">

.. figure:: connectivity/images/thumb/plot_canica_resting_state.png
    :target: ./connectivity/plot_canica_resting_state.html

    :ref:`example_connectivity_plot_canica_resting_state.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_canica_resting_state


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="This example extracts the signal on regions defined via a probabilistic atlas, to construct a f...">

.. figure:: connectivity/images/thumb/plot_probabilistic_atlas_extraction.png
    :target: ./connectivity/plot_probabilistic_atlas_extraction.html

    :ref:`example_connectivity_plot_probabilistic_atlas_extraction.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_probabilistic_atlas_extraction


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="Here we show how to extract signals from a brain parcellation and compute a correlation matrix.">

.. figure:: connectivity/images/thumb/plot_signal_extraction.png
    :target: ./connectivity/plot_signal_extraction.html

    :ref:`example_connectivity_plot_signal_extraction.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_signal_extraction


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="This example extract brain signals from spheres described by the coordinates of their center in...">

.. figure:: connectivity/images/thumb/plot_adhd_spheres.png
    :target: ./connectivity/plot_adhd_spheres.html

    :ref:`example_connectivity_plot_adhd_spheres.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_adhd_spheres


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="An example applying ICA to resting-state data. ">

.. figure:: connectivity/images/thumb/plot_ica_resting_state.png
    :target: ./connectivity/plot_ica_resting_state.html

    :ref:`example_connectivity_plot_ica_resting_state.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_ica_resting_state


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="This example shows a comparison of graph lasso and group-sparse covariance estimation of connec...">

.. figure:: connectivity/images/thumb/plot_simulated_connectome.png
    :target: ./connectivity/plot_simulated_connectome.html

    :ref:`example_connectivity_plot_simulated_connectome.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_simulated_connectome


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="This example constructs a functional connectome using the sparse inverse covariance.">

.. figure:: connectivity/images/thumb/plot_inverse_covariance_connectome.png
    :target: ./connectivity/plot_inverse_covariance_connectome.html

    :ref:`example_connectivity_plot_inverse_covariance_connectome.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_inverse_covariance_connectome


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="We use spatially-constrained Ward-clustering to create a set of parcels. These parcels are part...">

.. figure:: connectivity/images/thumb/plot_rest_clustering.png
    :target: ./connectivity/plot_rest_clustering.html

    :ref:`example_connectivity_plot_rest_clustering.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_rest_clustering


.. raw:: html

    <div class="sphx-glr-thumbContainer" tooltip="This example shows how to estimate a connectome on a groupe of subjects using the group sparse ...">

.. figure:: connectivity/images/thumb/plot_multi_subject_connectome.png
    :target: ./connectivity/plot_multi_subject_connectome.html

    :ref:`example_connectivity_plot_multi_subject_connectome.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   connectivity/plot_multi_subject_connectome


.. raw:: html

    <div style='clear:both'></div>
    


Decoding and predicting from brain images
-----------------------------------------

See :ref:`decoding` for more details.