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<!DOCTYPE html>
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<title>Nistats: Functional MRI in Python — functional MRI for NeuroImaging</title>
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<h2>Functional MRI Neuro-Imaging in Python</h2>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">1. Introduction: Nistats in a nutshell</a><ul>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#what-is-nistats">1.1. What is Nistats?</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#a-primer-on-bold-fmri-data-analysis">1.2. A primer on BOLD-fMRI data analysis</a><ul>
<li class="toctree-l3"><a class="reference internal" href="introduction.html#what-is-fmri">1.2.1. What is fMRI ?</a></li>
<li class="toctree-l3"><a class="reference internal" href="introduction.html#fmri-data-modelling">1.2.2. fMRI data modelling</a></li>
<li class="toctree-l3"><a class="reference internal" href="introduction.html#fmri-statistical-analysis">1.2.3. fMRI statistical analysis</a></li>
<li class="toctree-l3"><a class="reference internal" href="introduction.html#multiple-comparisons">1.2.4. Multiple Comparisons</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#tutorials">1.3. Tutorials</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#installing-nistats">1.4. Installing Nistats</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="auto_examples/index.html">2. Nistats usage examples</a><ul>
<li class="toctree-l2"><a class="reference internal" href="auto_examples/index.html#tutorial-examples">2.1. Tutorial examples</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="auto_examples/index.html#first-level-analysis-examples">2.2. First level analysis examples</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="auto_examples/index.html#second-level-analysis-examples">2.3. Second level analysis examples</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="auto_examples/index.html#complete-examples">2.5. Complete examples</a><ul>
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<li class="toctree-l1"><a class="reference internal" href="modules/reference.html">3. Reference documentation: all nistats functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.datasets">3.1. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.datasets</span></code>: Datasets</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_language_localizer_demo_dataset.html">3.1.1. nistats.datasets.fetch_language_localizer_demo_dataset</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_language_localizer_demo_dataset.html#examples-using-nistats-datasets-fetch-language-localizer-demo-dataset">3.1.1.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.datasets.fetch_language_localizer_demo_dataset</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_openneuro_dataset_index.html">3.1.2. nistats.datasets.fetch_openneuro_dataset_index</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_openneuro_dataset_index.html#examples-using-nistats-datasets-fetch-openneuro-dataset-index">3.1.2.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.datasets.fetch_openneuro_dataset_index</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.datasets.select_from_index.html">3.1.3. nistats.datasets.select_from_index</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.datasets.select_from_index.html#examples-using-nistats-datasets-select-from-index">3.1.3.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.datasets.select_from_index</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_openneuro_dataset.html">3.1.4. nistats.datasets.fetch_openneuro_dataset</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_openneuro_dataset.html#examples-using-nistats-datasets-fetch-openneuro-dataset">3.1.4.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.datasets.fetch_openneuro_dataset</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_localizer_first_level.html">3.1.5. nistats.datasets.fetch_localizer_first_level</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_localizer_first_level.html#examples-using-nistats-datasets-fetch-localizer-first-level">3.1.5.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.datasets.fetch_localizer_first_level</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_spm_auditory.html">3.1.6. nistats.datasets.fetch_spm_auditory</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_spm_auditory.html#examples-using-nistats-datasets-fetch-spm-auditory">3.1.6.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.datasets.fetch_spm_auditory</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_spm_multimodal_fmri.html">3.1.7. nistats.datasets.fetch_spm_multimodal_fmri</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_spm_multimodal_fmri.html#examples-using-nistats-datasets-fetch-spm-multimodal-fmri">3.1.7.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.datasets.fetch_spm_multimodal_fmri</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_fiac_first_level.html">3.1.8. nistats.datasets.fetch_fiac_first_level</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.datasets.fetch_fiac_first_level.html#examples-using-nistats-datasets-fetch-fiac-first-level">3.1.8.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.datasets.fetch_fiac_first_level</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.hemodynamic_models">3.2. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.hemodynamic_models</span></code>: Hemodynamic Models</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.hemodynamic_models.spm_hrf.html">3.2.1. nistats.hemodynamic_models.spm_hrf</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.hemodynamic_models.glover_hrf.html">3.2.2. nistats.hemodynamic_models.glover_hrf</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.hemodynamic_models.spm_time_derivative.html">3.2.3. nistats.hemodynamic_models.spm_time_derivative</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.hemodynamic_models.glover_time_derivative.html">3.2.4. nistats.hemodynamic_models.glover_time_derivative</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.hemodynamic_models.spm_dispersion_derivative.html">3.2.5. nistats.hemodynamic_models.spm_dispersion_derivative</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.hemodynamic_models.glover_dispersion_derivative.html">3.2.6. nistats.hemodynamic_models.glover_dispersion_derivative</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.hemodynamic_models.compute_regressor.html">3.2.7. nistats.hemodynamic_models.compute_regressor</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.hemodynamic_models.compute_regressor.html#examples-using-nistats-hemodynamic-models-compute-regressor">3.2.7.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.hemodynamic_models.compute_regressor</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.design_matrix">3.3. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.design_matrix</span></code>: Design Matrix Creation</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.design_matrix.make_first_level_design_matrix.html">3.3.1. nistats.design_matrix.make_first_level_design_matrix</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.design_matrix.make_first_level_design_matrix.html#examples-using-nistats-design-matrix-make-first-level-design-matrix">3.3.1.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.design_matrix.make_first_level_design_matrix</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.design_matrix.check_design_matrix.html">3.3.2. nistats.design_matrix.check_design_matrix</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.design_matrix.make_second_level_design_matrix.html">3.3.3. nistats.design_matrix.make_second_level_design_matrix</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.design_matrix.make_second_level_design_matrix.html#examples-using-nistats-design-matrix-make-second-level-design-matrix">3.3.3.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.design_matrix.make_second_level_design_matrix</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.experimental_paradigm">3.4. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.experimental_paradigm</span></code>: Experimental Paradigm</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.experimental_paradigm.check_events.html">3.4.1. nistats.experimental_paradigm.check_events</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.model">3.5. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.model</span></code>: Statistical models</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.model.LikelihoodModelResults.html">3.5.1. nistats.model.LikelihoodModelResults</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.model.TContrastResults.html">3.5.2. nistats.model.TContrastResults</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.model.FContrastResults.html">3.5.3. nistats.model.FContrastResults</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.regression">3.6. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.regression</span></code>: Regression Models</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.regression.OLSModel.html">3.6.1. nistats.regression.OLSModel</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.regression.ARModel.html">3.6.2. nistats.regression.ARModel</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.regression.RegressionResults.html">3.6.3. nistats.regression.RegressionResults</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.regression.SimpleRegressionResults.html">3.6.4. nistats.regression.SimpleRegressionResults</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.first_level_model">3.7. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.first_level_model</span></code>: First Level Model</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.first_level_model.FirstLevelModel.html">3.7.1. nistats.first_level_model.FirstLevelModel</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.first_level_model.FirstLevelModel.html#examples-using-nistats-first-level-model-firstlevelmodel">3.7.1.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.first_level_model.FirstLevelModel</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.first_level_model.mean_scaling.html">3.7.2. nistats.first_level_model.mean_scaling</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.first_level_model.run_glm.html">3.7.3. nistats.first_level_model.run_glm</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.first_level_model.run_glm.html#examples-using-nistats-first-level-model-run-glm">3.7.3.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.first_level_model.run_glm</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.first_level_model.first_level_models_from_bids.html">3.7.4. nistats.first_level_model.first_level_models_from_bids</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.first_level_model.first_level_models_from_bids.html#examples-using-nistats-first-level-model-first-level-models-from-bids">3.7.4.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.first_level_model.first_level_models_from_bids</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.second_level_model">3.8. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.second_level_model</span></code>: Second Level Model</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.second_level_model.SecondLevelModel.html">3.8.1. nistats.second_level_model.SecondLevelModel</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.second_level_model.SecondLevelModel.html#examples-using-nistats-second-level-model-secondlevelmodel">3.8.1.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.second_level_model.SecondLevelModel</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.contrasts">3.9. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.contrasts</span></code>: Contrasts</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.contrasts.Contrast.html">3.9.1. nistats.contrasts.Contrast</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.contrasts.Contrast.html#examples-using-nistats-contrasts-contrast">3.9.1.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.contrasts.Contrast</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.contrasts.compute_contrast.html">3.9.2. nistats.contrasts.compute_contrast</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.contrasts.compute_contrast.html#examples-using-nistats-contrasts-compute-contrast">3.9.2.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.contrasts.compute_contrast</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.thresholding">3.10. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.thresholding</span></code>: Thresholding Maps</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.thresholding.fdr_threshold.html">3.10.1. nistats.thresholding.fdr_threshold</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.thresholding.map_threshold.html">3.10.2. nistats.thresholding.map_threshold</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.thresholding.map_threshold.html#examples-using-nistats-thresholding-map-threshold">3.10.2.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.thresholding.map_threshold</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.reporting">3.11. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.reporting</span></code>: Report plotting functions</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.reporting.compare_niimgs.html">3.11.1. nistats.reporting.compare_niimgs</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.reporting.compare_niimgs.html#examples-using-nistats-reporting-compare-niimgs">3.11.1.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.reporting.compare_niimgs</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.reporting.plot_design_matrix.html">3.11.2. nistats.reporting.plot_design_matrix</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.reporting.plot_design_matrix.html#examples-using-nistats-reporting-plot-design-matrix">3.11.2.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.reporting.plot_design_matrix</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.reporting.plot_contrast_matrix.html">3.11.3. nistats.reporting.plot_contrast_matrix</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.reporting.plot_contrast_matrix.html#examples-using-nistats-reporting-plot-contrast-matrix">3.11.3.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.reporting.plot_contrast_matrix</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.reporting.get_clusters_table.html">3.11.4. nistats.reporting.get_clusters_table</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.reporting.get_clusters_table.html#examples-using-nistats-reporting-get-clusters-table">3.11.4.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.reporting.get_clusters_table</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.reporting.make_glm_report.html">3.11.5. nistats.reporting.make_glm_report</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/nistats.reporting.make_glm_report.html#examples-using-nistats-reporting-make-glm-report">3.11.5.1. Examples using <code class="docutils literal notranslate"><span class="pre">nistats.reporting.make_glm_report</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-nistats.utils">3.12. <code class="xref py py-mod docutils literal notranslate"><span class="pre">nistats.utils</span></code>: Utility functions</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.utils.z_score.html">3.12.1. nistats.utils.z_score</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.utils.multiple_fast_inverse.html">3.12.2. nistats.utils.multiple_fast_inverse</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.utils.multiple_mahalanobis.html">3.12.3. nistats.utils.multiple_mahalanobis</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.utils.full_rank.html">3.12.4. nistats.utils.full_rank</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.utils.positive_reciprocal.html">3.12.5. nistats.utils.positive_reciprocal</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.utils.get_bids_files.html">3.12.6. nistats.utils.get_bids_files</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/nistats.utils.parse_bids_filename.html">3.12.7. nistats.utils.parse_bids_filename</a></li>
</ul>
</li>
</ul>
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