:orphan:



.. _sphx_glr_auto_examples:

Nilearn usage 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>`.


.. contents:: **Contents**
    :local:
    :depth: 1

.. _tutorial_examples:

Tutorial examples
------------------

Introductory examples that teach how to use nilearn.



.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_plot_python_101_thumb.png
     :alt: Basic numerics and plotting with Python

     :ref:`sphx_glr_auto_examples_plot_python_101.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/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...">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_plot_nilearn_101_thumb.png
     :alt: Basic nilearn example: manipulating and looking at data

     :ref:`sphx_glr_auto_examples_plot_nilearn_101.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/plot_nilearn_101

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we discover how to work with 3D and 4D niimgs.">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_plot_3d_and_4d_niimg_thumb.png
     :alt: 3D and 4D niimgs: handling and visualizing

     :ref:`sphx_glr_auto_examples_plot_3d_and_4d_niimg.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/plot_3d_and_4d_niimg

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here is a simple tutorial on decoding with nilearn. It reproduces the Haxby 2001 study on a fac...">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_plot_decoding_tutorial_thumb.png
     :alt: A introduction tutorial to fMRI decoding

     :ref:`sphx_glr_auto_examples_plot_decoding_tutorial.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/plot_decoding_tutorial

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this tutorial, we use a General Linear Model (:term:`GLM`) to compare the fMRI signal during...">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_plot_single_subject_single_run_thumb.png
     :alt: Intro to GLM Analysis: a single-session, single-subject fMRI dataset

     :ref:`sphx_glr_auto_examples_plot_single_subject_single_run.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/plot_single_subject_single_run
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_01_plotting:

Visualization of brain images
-----------------------------

See :ref:`plotting` for more details.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="See plotting for more plotting functionalities.">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_demo_glass_brain_thumb.png
     :alt: Glass brain plotting in nilearn

     :ref:`sphx_glr_auto_examples_01_plotting_plot_demo_glass_brain.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_demo_glass_brain

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to fetch network matrices data from HCP beta-release of the Functional C...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_visualize_megatrawls_netmats_thumb.png
     :alt: Visualizing Megatrawls Network Matrices from Human Connectome Project

     :ref:`sphx_glr_auto_examples_01_plotting_plot_visualize_megatrawls_netmats.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_visualize_megatrawls_netmats

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Plot the regions of a reference atlas (Harvard-Oxford and Juelich atlases).">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_atlas_thumb.png
     :alt: Basic Atlas plotting

     :ref:`sphx_glr_auto_examples_01_plotting_plot_atlas.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_atlas

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to download and fetch brain parcellations of multiple networks using nil...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_multiscale_parcellations_thumb.png
     :alt: Visualizing multiscale functional brain parcellations

     :ref:`sphx_glr_auto_examples_01_plotting_plot_multiscale_parcellations.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_multiscale_parcellations

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Visualize HCP connectome workbench color maps shipped with Nilearn which can be used for plotti...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_colormaps_thumb.png
     :alt: Matplotlib colormaps in Nilearn

     :ref:`sphx_glr_auto_examples_01_plotting_plot_colormaps.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_colormaps

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Visualizing a probabilistic atlas requires visualizing the different maps that compose it.">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_overlay_thumb.png
     :alt: Visualizing a probabilistic atlas: the default mode in the MSDL atlas

     :ref:`sphx_glr_auto_examples_01_plotting_plot_overlay.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_overlay

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The dim argument controls the contrast of the background.">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_dim_plotting_thumb.png
     :alt: Controlling the contrast of the background when plotting

     :ref:`sphx_glr_auto_examples_01_plotting_plot_dim_plotting.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_dim_plotting

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Simple example to show Nifti data visualization.">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_visualization_thumb.png
     :alt: NeuroImaging volumes visualization

     :ref:`sphx_glr_auto_examples_01_plotting_plot_visualization.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_visualization

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A common quality control step for functional MRI data is to visualize the data over time in a c...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_carpet_thumb.png
     :alt: Visualizing global patterns with a carpet plot

     :ref:`sphx_glr_auto_examples_01_plotting_plot_carpet.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_carpet

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Small script to plot the masks of the Haxby dataset.">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_haxby_masks_thumb.png
     :alt: Plot Haxby masks

     :ref:`sphx_glr_auto_examples_01_plotting_plot_haxby_masks.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_haxby_masks

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In nilearn, nilearn.surface.vol_to_surf allows us to measure values of a 3d volume at the nodes...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_surface_projection_strategies_thumb.png
     :alt: Technical point: Illustration of the volume to surface sampling schemes

     :ref:`sphx_glr_auto_examples_01_plotting_plot_surface_projection_strategies.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_surface_projection_strategies

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Nilearn comes with a set of plotting functions for easy visualization of Nifti-like images such...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_demo_plotting_thumb.png
     :alt: Plotting tools in nilearn

     :ref:`sphx_glr_auto_examples_01_plotting_plot_demo_plotting.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_demo_plotting

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to visualize probabilistic atlases made of 4D images. There are 3 differ...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_prob_atlas_thumb.png
     :alt: Visualizing 4D probabilistic atlas maps

     :ref:`sphx_glr_auto_examples_01_plotting_plot_prob_atlas.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_prob_atlas

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The dataset that is a subset of the enhanced NKI Rockland sample (http://fcon_1000.projects.nit...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_surf_stat_map_thumb.png
     :alt: Seed-based connectivity on the surface

     :ref:`sphx_glr_auto_examples_01_plotting_plot_surf_stat_map.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_surf_stat_map

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The Destrieux parcellation (Destrieux et al, 2010) in fsaverage5 space as distributed with Free...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_surf_atlas_thumb.png
     :alt: Loading and plotting of a cortical surface atlas

     :ref:`sphx_glr_auto_examples_01_plotting_plot_surf_atlas.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_surf_atlas

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we will project a 3D statistical map onto a cortical mesh using vol_to_surf, d...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_3d_map_to_surface_projection_thumb.png
     :alt: Making a surface plot of a 3D statistical map

     :ref:`sphx_glr_auto_examples_01_plotting_plot_3d_map_to_surface_projection.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_3d_map_to_surface_projection

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The first part of this example goes through different options of the plot_glass_brain function ...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_demo_glass_brain_extensive_thumb.png
     :alt: Glass brain plotting in nilearn (all options)

     :ref:`sphx_glr_auto_examples_01_plotting_plot_demo_glass_brain_extensive.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_demo_glass_brain_extensive

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we show how to use some plotting options available with plotting functions of ...">

.. only:: html

 .. figure:: /auto_examples/01_plotting/images/thumb/sphx_glr_plot_demo_more_plotting_thumb.png
     :alt: More plotting tools from nilearn

     :ref:`sphx_glr_auto_examples_01_plotting_plot_demo_more_plotting.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/01_plotting/plot_demo_more_plotting
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_02_decoding:

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

See :ref:`decoding` for more details.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this script we plot an overview of the stimuli used in &quot;Distributed and Overlapping Represen...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_stimuli_thumb.png
     :alt: Show stimuli of Haxby et al. dataset

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_stimuli.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_stimuli

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we use fast ensembling of regularized models (FREM) to solve a regression prob...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_mixed_gambles_frem_thumb.png
     :alt: FREM on Jimura et al "mixed gambles" dataset.

     :ref:`sphx_glr_auto_examples_02_decoding_plot_mixed_gambles_frem.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_mixed_gambles_frem

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example uses fast ensembling of regularized models (FREM) to decode a face vs house discri...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_frem_thumb.png
     :alt: Decoding with FREM: face vs house object recognition

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_frem.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_frem

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Predicting age from gray-matter concentration maps from OASIS dataset. Note that age is a conti...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_oasis_vbm_space_net_thumb.png
     :alt: Voxel-Based Morphometry on Oasis dataset with Space-Net prior

     :ref:`sphx_glr_auto_examples_02_decoding_plot_oasis_vbm_space_net.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_oasis_vbm_space_net

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example does a simple but efficient decoding on the Haxby dataset: using a feature selecti...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_anova_svm_thumb.png
     :alt: Decoding with ANOVA + SVM: face vs house in the Haxby dataset

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_anova_svm.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_anova_svm

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This is a demo for surface-based searchlight decoding, as described in: Chen, Y., Namburi, P., ...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_searchlight_surface_thumb.png
     :alt: Cortical surface-based searchlight decoding

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_searchlight_surface.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_searchlight_surface

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="We compare one vs all and one vs one multi-class strategies: the overall cross-validated accura...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_multiclass_thumb.png
     :alt: The haxby dataset: different multi-class strategies

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_multiclass.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_multiclass

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Searchlight analysis requires fitting a classifier a large amount of times. As a result, it is ...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_searchlight_thumb.png
     :alt: Searchlight analysis of face vs house recognition

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_searchlight.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_searchlight

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Full step-by-step example of fitting a GLM to perform a decoding experiment. We use the data fr...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_glm_decoding_thumb.png
     :alt: Decoding of a dataset after GLM fit for signal extraction

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_glm_decoding.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_glm_decoding

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we set the number of features selected in an Anova-SVC approach to maximize the cross-vali...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_grid_search_thumb.png
     :alt: Setting a parameter by cross-validation

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_grid_search.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_grid_search

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this script we reproduce the data analysis conducted by Haxby et al. in &quot;Distributed and Ove...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_full_analysis_thumb.png
     :alt: ROI-based decoding analysis in Haxby et al. dataset

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_full_analysis.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_full_analysis

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we compare different classifiers on a visual object recognition decoding task.">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_haxby_different_estimators_thumb.png
     :alt: Different classifiers in decoding the Haxby dataset

     :ref:`sphx_glr_auto_examples_02_decoding_plot_haxby_different_estimators.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_haxby_different_estimators

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example uses Voxel-Based Morphometry (VBM) to study the relationship between aging and gra...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_oasis_vbm_thumb.png
     :alt: Voxel-Based Morphometry on Oasis dataset

     :ref:`sphx_glr_auto_examples_02_decoding_plot_oasis_vbm.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_oasis_vbm

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example simulates data according to a very simple sketch of brain imaging data and applies...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_simulated_data_thumb.png
     :alt: Example of pattern recognition on simulated data

     :ref:`sphx_glr_auto_examples_02_decoding_plot_simulated_data.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_simulated_data

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example partly reproduces the encoding model presented in     `Visual image reconstruction...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_miyawaki_encoding_thumb.png
     :alt: Encoding models for visual stimuli from Miyawaki et al. 2008

     :ref:`sphx_glr_auto_examples_02_decoding_plot_miyawaki_encoding.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_miyawaki_encoding

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example reproduces the experiment presented in     `Visual image reconstruction from human...">

.. only:: html

 .. figure:: /auto_examples/02_decoding/images/thumb/sphx_glr_plot_miyawaki_reconstruction_thumb.png
     :alt: Reconstruction of visual stimuli from Miyawaki et al. 2008

     :ref:`sphx_glr_auto_examples_02_decoding_plot_miyawaki_reconstruction.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/02_decoding/plot_miyawaki_reconstruction
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_03_connectivity:

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

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



.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_probabilistic_atlas_extraction_thumb.png
     :alt: Extracting signals of a probabilistic atlas of functional regions

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_probabilistic_atlas_extraction.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_probabilistic_atlas_extraction

.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_inverse_covariance_connectome_thumb.png
     :alt: Computing a connectome with sparse inverse covariance

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_inverse_covariance_connectome.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_inverse_covariance_connectome

.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_simulated_connectome_thumb.png
     :alt: Connectivity structure estimation on simulated data

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_simulated_connectome.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_simulated_connectome

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Various approaches exist to derive spatial maps or networks from group fmr data. The methods ex...">

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_compare_decomposition_thumb.png
     :alt: Deriving spatial maps from group fMRI data using ICA and Dictionary Learning

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_compare_decomposition.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_compare_decomposition

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to produce seed-to-:term:`voxel` correlation maps for a single subject b...">

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_seed_to_voxel_correlation_thumb.png
     :alt: Producing single subject maps of seed-to-voxel correlation

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_seed_to_voxel_correlation.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_seed_to_voxel_correlation

.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_multi_subject_connectome_thumb.png
     :alt: Group Sparse inverse covariance for multi-subject connectome

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_multi_subject_connectome.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_multi_subject_connectome

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use nilearn.regions.RegionExtractor to extract spatially constrained ...">

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_extract_regions_dictlearning_maps_thumb.png
     :alt: Regions extraction using :term:`Dictionary learning` and functional connectomes

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_extract_regions_dictlearning_maps.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_extract_regions_dictlearning_maps

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This examples shows how to turn a parcellation into connectome for visualization. This requires...">

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_atlas_comparison_thumb.png
     :alt: Comparing connectomes on different reference atlases

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_atlas_comparison.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_atlas_comparison

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example compares different kinds of functional connectivity between regions of interest : ...">

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_group_level_connectivity_thumb.png
     :alt: Classification of age groups using functional connectivity

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_group_level_connectivity.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_group_level_connectivity

.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_signal_extraction_thumb.png
     :alt: Extracting signals from a brain parcellation

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_signal_extraction.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_signal_extraction

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to extract signals from spherical regions. We show how to build spheres ...">

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_sphere_based_connectome_thumb.png
     :alt: Extract signals on spheres and plot a connectome

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_sphere_based_connectome.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_sphere_based_connectome

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="We use spatially-constrained Ward-clustering, KMeans, Hierarchical KMeans and Recursive Neighbo...">

.. only:: html

 .. figure:: /auto_examples/03_connectivity/images/thumb/sphx_glr_plot_data_driven_parcellations_thumb.png
     :alt: Clustering methods to learn a brain parcellation from fMRI

     :ref:`sphx_glr_auto_examples_03_connectivity_plot_data_driven_parcellations.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/03_connectivity/plot_data_driven_parcellations
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_04_glm_first_level:

GLM: First level analysis examples
-----------------------------------

These are examples focused on showcasing first level models functionality and single subject analysis.

See :ref:`glm` for more details.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a BIDS-compatible events.tsv file from onset/trial-type information.">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_write_events_file_thumb.png
     :alt: Generate an events.tsv file for the NeuroSpin localizer task

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_write_events_file.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_write_events_file

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how to run a fixed effects model based on pre-computed statistics. Thi...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_fixed_effects_thumb.png
     :alt: Example of explicit fixed effects fMRI model fitting

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_fixed_effects.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_fixed_effects

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a full step-by-step workflow of fitting a GLM to data extracted from a seed ...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_adhd_dmn_thumb.png
     :alt: Default Mode Network extraction of AHDH dataset

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_adhd_dmn.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_adhd_dmn

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Three examples of design matrices specification and computation for first-level fMRI data analy...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_design_matrix_thumb.png
     :alt: Examples of design matrices

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_design_matrix.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_design_matrix

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="FIR models are used to estimate the hemodyamic response non-parametrically. The example below s...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_fir_model_thumb.png
     :alt: Analysis of an fMRI dataset with a Finite Impule Response (FIR) model

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_fir_model.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_fir_model

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The example shows the analysis of an SPM dataset studying face perception.  The analysis is per...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_spm_multimodal_faces_thumb.png
     :alt: Single-subject data (two sessions) in native space

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_spm_multimodal_faces.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_spm_multimodal_faces

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Within this example we are going to plot the hemodynamic response function (:term:`HRF`) model ...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_hrf_thumb.png
     :alt: Example of MRI response functions

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_hrf.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_hrf

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here, we will go through a full step-by-step example of fitting a GLM to experimental data and ...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_fiac_analysis_thumb.png
     :alt: Simple example of two-session fMRI model fitting

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_fiac_analysis.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_fiac_analysis

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip=" Full step-by-step example of fitting a GLM to perform a first level analysis in an openneuro B...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_bids_features_thumb.png
     :alt: First level analysis of a complete BIDS dataset from openneuro

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_bids_features.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_bids_features

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we fit a First Level GLM with the minimize_memory-argument set to False. By doing so, the ...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_predictions_residuals_thumb.png
     :alt: Predicted time series and residuals

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_predictions_residuals.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_predictions_residuals

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A full step-by-step example of fitting a GLM to experimental data sampled on the cortical surfa...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_localizer_surface_analysis_thumb.png
     :alt: Example of surface-based first-level analysis

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_localizer_surface_analysis.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_localizer_surface_analysis

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this tutorial, we study how first-level models are parametrized for fMRI data analysis and c...">

.. only:: html

 .. figure:: /auto_examples/04_glm_first_level/images/thumb/sphx_glr_plot_first_level_details_thumb.png
     :alt: Understanding parameters of the first-level model

     :ref:`sphx_glr_auto_examples_04_glm_first_level_plot_first_level_details.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/04_glm_first_level/plot_first_level_details
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_05_glm_second_level:

GLM : Second level analysis examples
-------------------------------------

These are examples focused on showcasing second level models functionality and group level analysis.

See :ref:`glm` for more details.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how a second-level design matrix is specified: assuming that the data refer ...">

.. only:: html

 .. figure:: /auto_examples/05_glm_second_level/images/thumb/sphx_glr_plot_second_level_design_matrix_thumb.png
     :alt: Example of second level design matrix

     :ref:`sphx_glr_auto_examples_05_glm_second_level_plot_second_level_design_matrix.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/05_glm_second_level/plot_second_level_design_matrix

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script showcases the so-called &quot;All resolution inference&quot; procedure, in which the proporti...">

.. only:: html

 .. figure:: /auto_examples/05_glm_second_level/images/thumb/sphx_glr_plot_proportion_activated_voxels_thumb.png
     :alt: Second-level fMRI model: true positive proportion in clusters

     :ref:`sphx_glr_auto_examples_05_glm_second_level_plot_proportion_activated_voxels.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/05_glm_second_level/plot_proportion_activated_voxels

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Perform a one-sample t-test on a bunch of images (a.k.a. second-level analysis in fMRI) and thr...">

.. only:: html

 .. figure:: /auto_examples/05_glm_second_level/images/thumb/sphx_glr_plot_thresholding_thumb.png
     :alt: Statistical testing of a second-level analysis

     :ref:`sphx_glr_auto_examples_05_glm_second_level_plot_thresholding.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/05_glm_second_level/plot_thresholding

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example uses Voxel-Based Morphometry (VBM) to study the relationship between aging, sex an...">

.. only:: html

 .. figure:: /auto_examples/05_glm_second_level/images/thumb/sphx_glr_plot_oasis_thumb.png
     :alt: Voxel-Based Morphometry on Oasis dataset

     :ref:`sphx_glr_auto_examples_05_glm_second_level_plot_oasis.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/05_glm_second_level/plot_oasis

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Full step-by-step example of fitting a GLM to perform a second level analysis in experimental d...">

.. only:: html

 .. figure:: /auto_examples/05_glm_second_level/images/thumb/sphx_glr_plot_second_level_two_sample_test_thumb.png
     :alt: Second-level fMRI model: two-sample test, unpaired and paired

     :ref:`sphx_glr_auto_examples_05_glm_second_level_plot_second_level_two_sample_test.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/05_glm_second_level/plot_second_level_two_sample_test

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Full step-by-step example of fitting a GLM to perform a second-level analysis (one-sample test)...">

.. only:: html

 .. figure:: /auto_examples/05_glm_second_level/images/thumb/sphx_glr_plot_second_level_one_sample_test_thumb.png
     :alt: Second-level fMRI model: one sample test

     :ref:`sphx_glr_auto_examples_05_glm_second_level_plot_second_level_one_sample_test.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/05_glm_second_level/plot_second_level_one_sample_test

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows the results obtained in a group analysis using a more complex contrast than ...">

.. only:: html

 .. figure:: /auto_examples/05_glm_second_level/images/thumb/sphx_glr_plot_second_level_association_test_thumb.png
     :alt: Example of generic design in second-level models

     :ref:`sphx_glr_auto_examples_05_glm_second_level_plot_second_level_association_test.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/05_glm_second_level/plot_second_level_association_test
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_06_manipulating_images:

Manipulating brain image volumes
--------------------------------

See :ref:`data_manipulation` for more details.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The goal of this example is to illustrate the use of the function nilearn.image.math_img on T-m...">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_negate_image_thumb.png
     :alt: Negating an image with math_img

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_negate_image.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_negate_image

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The goal of this example is to illustrate the use of the function nilearn.image.math_img with a...">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_compare_mean_image_thumb.png
     :alt: Comparing the means of 2 images

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_compare_mean_image.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_compare_mean_image

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we smooth a mean EPI image and plot the result">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_smooth_mean_image_thumb.png
     :alt: Smoothing an image

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_smooth_mean_image.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_smooth_mean_image

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This simple example shows how to extract regions from Smith atlas resting state networks.">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_extract_rois_smith_atlas_thumb.png
     :alt: Regions Extraction of Default Mode Networks using Smith Atlas

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_extract_rois_smith_atlas.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_extract_rois_smith_atlas

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use nilearn.regions.connected_label_regions to assign each spatially-...">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_extract_regions_labels_image_thumb.png
     :alt: Breaking an atlas of labels in separated regions

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_extract_regions_labels_image.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_extract_regions_labels_image

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The goal of this example is to illustrate the use of the function nilearn.image.resample_to_img...">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_resample_to_template_thumb.png
     :alt: Resample an image to a template

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_resample_to_template.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_resample_to_template

.. 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...">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_nifti_simple_thumb.png
     :alt: Simple example of NiftiMasker use

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_nifti_simple.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_nifti_simple

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This simple example shows how to extract signals from functional fMRI data and brain regions de...">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_nifti_labels_simple_thumb.png
     :alt: Extracting signals from brain regions using the NiftiLabelsMasker

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_nifti_labels_simple.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_nifti_labels_simple

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to extract regions or separate the regions from a statistical map.">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_extract_rois_statistical_maps_thumb.png
     :alt: Region Extraction using a t-statistical map (3D)

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_extract_rois_statistical_maps.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_extract_rois_statistical_maps

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, the Nifti masker is used to automatically compute a mask.">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_mask_computation_thumb.png
     :alt: Understanding NiftiMasker and mask computation

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_mask_computation.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_mask_computation

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how an affine resampling works.">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_affine_transformation_thumb.png
     :alt: Visualization of affine resamplings

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_affine_transformation.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_affine_transformation

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows manual steps to create and further modify an ROI spatial mask. They represen...">

.. only:: html

 .. figure:: /auto_examples/06_manipulating_images/images/thumb/sphx_glr_plot_roi_extraction_thumb.png
     :alt: Computing a Region of Interest (ROI) mask manually

     :ref:`sphx_glr_auto_examples_06_manipulating_images_plot_roi_extraction.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/06_manipulating_images/plot_roi_extraction
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_07_advanced:

Advanced statistical analysis of brain images
---------------------------------------------



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip=" This example is meant to demonstrate nilearn as a low-level tools used to combine feature extr...">

.. only:: html

 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_ica_resting_state_thumb.png
     :alt: Multivariate decompositions: Independent component analysis of fMRI

     :ref:`sphx_glr_auto_examples_07_advanced_plot_ica_resting_state.py`

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   /auto_examples/07_advanced/plot_ica_resting_state

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

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_localizer_simple_analysis_thumb.png
     :alt: Massively univariate analysis of a calculation task from the Localizer dataset

     :ref:`sphx_glr_auto_examples_07_advanced_plot_localizer_simple_analysis.py`

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   /auto_examples/07_advanced/plot_localizer_simple_analysis

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    <div class="sphx-glr-thumbcontainer" tooltip=" Full step-by-step example of fitting a GLM to perform a first and second level analysis in a B...">

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_bids_analysis_thumb.png
     :alt: BIDS dataset first and second level analysis

     :ref:`sphx_glr_auto_examples_07_advanced_plot_bids_analysis.py`

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    <div class="sphx-glr-thumbcontainer" tooltip="This example compares different kinds of functional connectivity between regions of interest : ...">

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_age_group_prediction_cross_val_thumb.png
     :alt: Functional connectivity predicts age group

     :ref:`sphx_glr_auto_examples_07_advanced_plot_age_group_prediction_cross_val.py`

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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to download statistical maps from NeuroVault">

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_neurovault_meta_analysis_thumb.png
     :alt: NeuroVault meta-analysis of stop-go paradigm studies.

     :ref:`sphx_glr_auto_examples_07_advanced_plot_neurovault_meta_analysis.py`

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    <div class="sphx-glr-thumbcontainer" tooltip=" Full step-by-step example of fitting a GLM (first and second level analysis) in a 10-subjects ...">

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_surface_bids_analysis_thumb.png
     :alt: Surface-based dataset first and second level analysis of a dataset

     :ref:`sphx_glr_auto_examples_07_advanced_plot_surface_bids_analysis.py`

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_localizer_mass_univariate_methods_thumb.png
     :alt: Massively univariate analysis of a motor task from the Localizer dataset

     :ref:`sphx_glr_auto_examples_07_advanced_plot_localizer_mass_univariate_methods.py`

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   /auto_examples/07_advanced/plot_localizer_mass_univariate_methods

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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to download statistical maps from NeuroVault, label them with NeuroSynth...">

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_ica_neurovault_thumb.png
     :alt: NeuroVault cross-study ICA maps.

     :ref:`sphx_glr_auto_examples_07_advanced_plot_ica_neurovault.py`

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    <div class="sphx-glr-thumbcontainer" tooltip="A permuted Ordinary Least Squares algorithm is run at each voxel in order to determine whether ...">

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_haxby_mass_univariate_thumb.png
     :alt: Massively univariate analysis of face vs house recognition

     :ref:`sphx_glr_auto_examples_07_advanced_plot_haxby_mass_univariate.py`

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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial opens the box of decoding pipelines to bridge integrated functionalities provided...">

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_advanced_decoding_scikit_thumb.png
     :alt: Advanced decoding using scikit learn

     :ref:`sphx_glr_auto_examples_07_advanced_plot_advanced_decoding_scikit.py`

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 .. figure:: /auto_examples/07_advanced/images/thumb/sphx_glr_plot_beta_series_thumb.png
     :alt: Beta-Series Modeling for Task-Based Functional Connectivity and Decoding

     :ref:`sphx_glr_auto_examples_07_advanced_plot_beta_series.py`

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 .. container:: sphx-glr-footer
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    :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`



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    :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


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