:orphan:



.. _sphx_glr_auto_examples:

Nistats 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 nistats manually, make sure you have followed
    :ref:`the instructions <installation>`.


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


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



.. _sphx_glr_auto_examples_01_tutorials:

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

These are examples with detailed explanations to showcase how to perform an fMRI first and second level analysis in arbitrary datasets and BIDS datasets.



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    <div class="sphx-glr-thumbcontainer" tooltip="In this tutorial, we compare the fMRI signal during periods of auditory stimulation versus peri...">

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 .. figure:: /auto_examples/01_tutorials/images/thumb/sphx_glr_plot_single_subject_single_run_thumb.png

     :ref:`sphx_glr_auto_examples_01_tutorials_plot_single_subject_single_run.py`

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    </div>


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   /auto_examples/01_tutorials/plot_single_subject_single_run

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    <div class="sphx-glr-thumbcontainer" tooltip="In this tutorial, we study the parametrization of the first-level model used for fMRI data anal...">

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 .. figure:: /auto_examples/01_tutorials/images/thumb/sphx_glr_plot_first_level_model_details_thumb.png

     :ref:`sphx_glr_auto_examples_01_tutorials_plot_first_level_model_details.py`

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    </div>


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   /auto_examples/01_tutorials/plot_first_level_model_details
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_02_first_level_models:

First level analysis examples
------------------------------

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



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

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 .. figure:: /auto_examples/02_first_level_models/images/thumb/sphx_glr_plot_fixed_effects_thumb.png

     :ref:`sphx_glr_auto_examples_02_first_level_models_plot_fixed_effects.py`

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    </div>


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   /auto_examples/02_first_level_models/plot_fixed_effects

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    <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 ...">

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 .. figure:: /auto_examples/02_first_level_models/images/thumb/sphx_glr_plot_adhd_dmn_thumb.png

     :ref:`sphx_glr_auto_examples_02_first_level_models_plot_adhd_dmn.py`

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    </div>


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   /auto_examples/02_first_level_models/plot_adhd_dmn

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

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 .. figure:: /auto_examples/02_first_level_models/images/thumb/sphx_glr_plot_fir_model_thumb.png

     :ref:`sphx_glr_auto_examples_02_first_level_models_plot_fir_model.py`

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    </div>


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   /auto_examples/02_first_level_models/plot_fir_model

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

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 .. figure:: /auto_examples/02_first_level_models/images/thumb/sphx_glr_plot_spm_multimodal_faces_thumb.png

     :ref:`sphx_glr_auto_examples_02_first_level_models_plot_spm_multimodal_faces.py`

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    </div>


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   /auto_examples/02_first_level_models/plot_spm_multimodal_faces

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    <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 ...">

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 .. figure:: /auto_examples/02_first_level_models/images/thumb/sphx_glr_plot_fiac_analysis_thumb.png

     :ref:`sphx_glr_auto_examples_02_first_level_models_plot_fiac_analysis.py`

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    </div>


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   /auto_examples/02_first_level_models/plot_fiac_analysis

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    <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...">

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 .. figure:: /auto_examples/02_first_level_models/images/thumb/sphx_glr_plot_bids_features_thumb.png

     :ref:`sphx_glr_auto_examples_02_first_level_models_plot_bids_features.py`

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    </div>


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   /auto_examples/02_first_level_models/plot_bids_features

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    <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 ...">

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 .. figure:: /auto_examples/02_first_level_models/images/thumb/sphx_glr_plot_predictions_residuals_thumb.png

     :ref:`sphx_glr_auto_examples_02_first_level_models_plot_predictions_residuals.py`

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    </div>


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   /auto_examples/02_first_level_models/plot_predictions_residuals

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

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 .. figure:: /auto_examples/02_first_level_models/images/thumb/sphx_glr_plot_localizer_surface_analysis_thumb.png

     :ref:`sphx_glr_auto_examples_02_first_level_models_plot_localizer_surface_analysis.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/02_first_level_models/plot_localizer_surface_analysis
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_03_second_level_models:

Second level analysis examples
------------------------------

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



.. raw:: html

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

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 .. figure:: /auto_examples/03_second_level_models/images/thumb/sphx_glr_plot_proportion_activated_voxels_thumb.png

     :ref:`sphx_glr_auto_examples_03_second_level_models_plot_proportion_activated_voxels.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/03_second_level_models/plot_proportion_activated_voxels

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

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 .. figure:: /auto_examples/03_second_level_models/images/thumb/sphx_glr_plot_second_level_two_sample_test_thumb.png

     :ref:`sphx_glr_auto_examples_03_second_level_models_plot_second_level_two_sample_test.py`

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    </div>


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   :hidden:

   /auto_examples/03_second_level_models/plot_second_level_two_sample_test

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

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 .. figure:: /auto_examples/03_second_level_models/images/thumb/sphx_glr_plot_thresholding_thumb.png

     :ref:`sphx_glr_auto_examples_03_second_level_models_plot_thresholding.py`

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    </div>


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   /auto_examples/03_second_level_models/plot_thresholding

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

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 .. figure:: /auto_examples/03_second_level_models/images/thumb/sphx_glr_plot_oasis_thumb.png

     :ref:`sphx_glr_auto_examples_03_second_level_models_plot_oasis.py`

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    </div>


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   /auto_examples/03_second_level_models/plot_oasis

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

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 .. figure:: /auto_examples/03_second_level_models/images/thumb/sphx_glr_plot_second_level_one_sample_test_thumb.png

     :ref:`sphx_glr_auto_examples_03_second_level_models_plot_second_level_one_sample_test.py`

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    </div>


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   /auto_examples/03_second_level_models/plot_second_level_one_sample_test

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

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 .. figure:: /auto_examples/03_second_level_models/images/thumb/sphx_glr_plot_second_level_association_test_thumb.png

     :ref:`sphx_glr_auto_examples_03_second_level_models_plot_second_level_association_test.py`

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    </div>


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   /auto_examples/03_second_level_models/plot_second_level_association_test
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_04_low_level_functions:

Low level function examples
----------------------------

These are examples focused on showcasing low level functionality like design matrix creation, HRF functions and others.



.. raw:: html

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

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 .. figure:: /auto_examples/04_low_level_functions/images/thumb/sphx_glr_plot_second_level_design_matrix_thumb.png

     :ref:`sphx_glr_auto_examples_04_low_level_functions_plot_second_level_design_matrix.py`

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    </div>


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   :hidden:

   /auto_examples/04_low_level_functions/plot_second_level_design_matrix

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    <div class="sphx-glr-thumbcontainer" tooltip="Within this example we are going to plot the hemodynamic reponse function (hrf) model in SPM to...">

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 .. figure:: /auto_examples/04_low_level_functions/images/thumb/sphx_glr_plot_hrf_thumb.png

     :ref:`sphx_glr_auto_examples_04_low_level_functions_plot_hrf.py`

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   /auto_examples/04_low_level_functions/plot_hrf

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    <div class="sphx-glr-thumbcontainer" tooltip="The protocol described is the so-called &quot;archi standard&quot; localizer event sequence.  See Pinel e...">

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 .. figure:: /auto_examples/04_low_level_functions/images/thumb/sphx_glr_write_events_file_thumb.png

     :ref:`sphx_glr_auto_examples_04_low_level_functions_write_events_file.py`

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    </div>


.. toctree::
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   /auto_examples/04_low_level_functions/write_events_file

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

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 .. figure:: /auto_examples/04_low_level_functions/images/thumb/sphx_glr_plot_design_matrix_thumb.png

     :ref:`sphx_glr_auto_examples_04_low_level_functions_plot_design_matrix.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/04_low_level_functions/plot_design_matrix
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_05_complete_examples:

Complete examples
-----------------

Complete step-by-step examples, including First and Second Level Models.



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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/05_complete_examples/images/thumb/sphx_glr_plot_bids_analysis_thumb.png

     :ref:`sphx_glr_auto_examples_05_complete_examples_plot_bids_analysis.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/05_complete_examples/plot_bids_analysis

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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/05_complete_examples/images/thumb/sphx_glr_plot_surface_bids_analysis_thumb.png

     :ref:`sphx_glr_auto_examples_05_complete_examples_plot_surface_bids_analysis.py`

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    </div>


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   :hidden:

   /auto_examples/05_complete_examples/plot_surface_bids_analysis

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    <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...">

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 .. figure:: /auto_examples/05_complete_examples/images/thumb/sphx_glr_plot_haxby_block_classification_thumb.png

     :ref:`sphx_glr_auto_examples_05_complete_examples_plot_haxby_block_classification.py`

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    </div>


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   /auto_examples/05_complete_examples/plot_haxby_block_classification
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    <div class="sphx-glr-clear"></div>



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 .. container:: sphx-glr-footer
    :class: sphx-glr-footer-gallery


  .. container:: sphx-glr-download

    :download:`Download all examples in Python source code: auto_examples_python.zip <//home/kshitij/workspace/nistats-org/nistats-repo/nistats-kchawla-pi/doc/auto_examples/auto_examples_python.zip>`



  .. container:: sphx-glr-download

    :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip <//home/kshitij/workspace/nistats-org/nistats-repo/nistats-kchawla-pi/doc/auto_examples/auto_examples_jupyter.zip>`


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

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