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<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_haxby_anova_svm.html">Decoding with ANOVA + SVM: face vs house in the Haxby dataset</a></li>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_haxby_searchlight_surface.html">Cortical surface-based searchlight decoding</a></li>
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<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_haxby_searchlight.html">Searchlight analysis of face vs house recognition</a></li>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_haxby_glm_decoding.html">Decoding of a dataset after GLM fit for signal extraction</a></li>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_haxby_grid_search.html">Setting a parameter by cross-validation</a></li>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_haxby_full_analysis.html">ROI-based decoding analysis in Haxby et al. dataset</a></li>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_haxby_different_estimators.html">Different classifiers in decoding the Haxby dataset</a></li>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_oasis_vbm.html">Voxel-Based Morphometry on Oasis dataset</a></li>
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<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_miyawaki_encoding.html">Encoding models for visual stimuli from Miyawaki et al. 2008</a></li>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/02_decoding/plot_miyawaki_reconstruction.html">Reconstruction of visual stimuli from Miyawaki et al. 2008</a></li>
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<li class="toctree-l2 has-children"><a class="reference internal" href="auto_examples/03_connectivity/index.html">Functional connectivity</a><input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" role="switch" type="checkbox"/><label for="toctree-checkbox-5"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/03_connectivity/plot_probabilistic_atlas_extraction.html">Extracting signals of a probabilistic atlas of functional regions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="auto_examples/03_connectivity/plot_multi_subject_connectome.html">Group Sparse inverse covariance for multi-subject connectome</a></li>
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<li class="toctree-l3"><a class="reference internal" href="auto_examples/05_glm_second_level/plot_second_level_association_test.html">Example of generic design in second-level models</a></li>
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<li class="toctree-l3"><a class="reference internal" href="auto_examples/06_manipulating_images/plot_nifti_simple.html">Simple example of NiftiMasker use</a></li>
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<li class="toctree-l3"><a class="reference internal" href="auto_examples/06_manipulating_images/plot_extract_rois_statistical_maps.html">Region Extraction using a t-statistical map (3D)</a></li>
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<li class="toctree-l3"><a class="reference internal" href="auto_examples/07_advanced/plot_advanced_decoding_scikit.html">Advanced decoding using scikit learn</a></li>
<li class="toctree-l3"><a class="reference internal" href="auto_examples/07_advanced/plot_beta_series.html">Beta-Series Modeling for Task-Based Functional Connectivity and Decoding</a></li>
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<li class="toctree-l2"><a class="reference internal" href="introduction.html">Introduction</a></li>
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<li class="toctree-l3"><a class="reference internal" href="building_blocks/manual_pipeline.html">Building your own neuroimaging machine-learning pipeline</a></li>
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<li class="toctree-l2 has-children"><a class="reference internal" href="modules/connectome.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.connectome</span></code>: Functional Connectivity</a><input class="toctree-checkbox" id="toctree-checkbox-18" name="toctree-checkbox-18" role="switch" type="checkbox"/><label for="toctree-checkbox-18"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2 has-children"><a class="reference internal" href="modules/regions.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.regions</span></code>: Operating on Regions</a><input class="toctree-checkbox" id="toctree-checkbox-29" name="toctree-checkbox-29" role="switch" type="checkbox"/><label for="toctree-checkbox-29"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<p class="caption" role="heading"><span class="caption-text">Development</span></p>
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<article role="main">
<section id="migrating-from-nistats">
<span id="nistats-migration"></span><h1>Migrating from Nistats<a class="headerlink" href="#migrating-from-nistats" title="Permalink to this heading">#</a></h1>
<p>A quick guide to changing your Nistats imports to work in Nilearn</p>
<section id="datasets">
<h2>Datasets<a class="headerlink" href="#datasets" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.datasets">nistats.datasets</a>
are in <a class="reference internal" href="modules/datasets.html#module-nilearn.datasets" title="nilearn.datasets"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.datasets</span></code></a></p>
</section>
<section id="hemodynamic-models">
<h2>Hemodynamic Models<a class="headerlink" href="#hemodynamic-models" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.hemodynamic_models">nistats.hemodynamic_models</a>
are in <a class="reference internal" href="modules/glm.html#module-nilearn.glm.first_level" title="nilearn.glm.first_level"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm.first_level</span></code></a></p>
</section>
<section id="design-matrix">
<h2>Design matrix<a class="headerlink" href="#design-matrix" title="Permalink to this heading">#</a></h2>
<p>Most imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.design_matrix">nistats.design_matrix</a>
are in <a class="reference internal" href="modules/glm.html#module-nilearn.glm.first_level" title="nilearn.glm.first_level"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm.first_level</span></code></a></p>
<p><a class="reference external" href="https://nistats.github.io/modules/generated/nistats.design_matrix.make_second_level_design_matrix.html#nistats.design_matrix.make_second_level_design_matrix">nistats.design_matrix.make_second_level_design_matrix</a>
is in <a class="reference internal" href="modules/glm.html#module-nilearn.glm.second_level" title="nilearn.glm.second_level"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm.second_level</span></code></a></p>
</section>
<section id="experimental-paradigm">
<h2>Experimental Paradigm<a class="headerlink" href="#experimental-paradigm" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.experimental_paradigm">nistats.experimental_paradigm</a> are in <a class="reference internal" href="modules/glm.html#module-nilearn.glm.first_level" title="nilearn.glm.first_level"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm.first_level</span></code></a></p>
</section>
<section id="statistical-models">
<h2>Statistical Models<a class="headerlink" href="#statistical-models" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.model">nistats.model</a>
are now in <a class="reference internal" href="modules/glm.html#module-nilearn.glm" title="nilearn.glm"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm</span></code></a></p>
</section>
<section id="regression-models">
<h2>Regression Models<a class="headerlink" href="#regression-models" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.regression">nistats.regression</a>
are in <a class="reference internal" href="modules/glm.html#module-nilearn.glm" title="nilearn.glm"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm</span></code></a></p>
</section>
<section id="first-level-model">
<h2>First Level Model<a class="headerlink" href="#first-level-model" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.first_level">nistats.first_level</a>
are in <a class="reference internal" href="modules/glm.html#module-nilearn.glm.first_level" title="nilearn.glm.first_level"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm.first_level</span></code></a></p>
</section>
<section id="second-level-model">
<h2>Second Level Model<a class="headerlink" href="#second-level-model" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.second_level">nistats.second_level</a>
are in <a class="reference internal" href="modules/glm.html#module-nilearn.glm.second_level" title="nilearn.glm.second_level"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm.second_level</span></code></a></p>
</section>
<section id="contrasts">
<h2>Contrasts<a class="headerlink" href="#contrasts" title="Permalink to this heading">#</a></h2>
<p>imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.contrasts">nistats.contrasts</a>
are in <a class="reference internal" href="modules/glm.html#module-nilearn.glm" title="nilearn.glm"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm</span></code></a></p>
</section>
<section id="thresholding-maps">
<h2>Thresholding Maps<a class="headerlink" href="#thresholding-maps" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.thresholding">nistats.thresholding</a>
are in <a class="reference internal" href="modules/glm.html#module-nilearn.glm" title="nilearn.glm"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.glm</span></code></a></p>
</section>
<section id="report-plotting-functions">
<h2>Report plotting functions<a class="headerlink" href="#report-plotting-functions" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.reporting">nistats.reporting</a>
are in <a class="reference internal" href="modules/reporting.html#module-nilearn.reporting" title="nilearn.reporting"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.reporting</span></code></a> or <a class="reference internal" href="modules/plotting.html#module-nilearn.plotting" title="nilearn.plotting"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.plotting</span></code></a></p>
</section>
<section id="utility-functions">
<h2>Utility functions<a class="headerlink" href="#utility-functions" title="Permalink to this heading">#</a></h2>
<p>Imports from
<a class="reference external" href="https://nistats.github.io/modules/reference.html#module-nistats.utils">nistats.utils</a>
are in <cite>nilearn._utils</cite> and are usually meant for development purposes.</p>
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Contents
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<ul>
<li><a class="reference internal" href="#">Migrating from Nistats</a><ul>
<li><a class="reference internal" href="#datasets">Datasets</a></li>
<li><a class="reference internal" href="#hemodynamic-models">Hemodynamic Models</a></li>
<li><a class="reference internal" href="#design-matrix">Design matrix</a></li>
<li><a class="reference internal" href="#experimental-paradigm">Experimental Paradigm</a></li>
<li><a class="reference internal" href="#statistical-models">Statistical Models</a></li>
<li><a class="reference internal" href="#regression-models">Regression Models</a></li>
<li><a class="reference internal" href="#first-level-model">First Level Model</a></li>
<li><a class="reference internal" href="#second-level-model">Second Level Model</a></li>
<li><a class="reference internal" href="#contrasts">Contrasts</a></li>
<li><a class="reference internal" href="#thresholding-maps">Thresholding Maps</a></li>
<li><a class="reference internal" href="#report-plotting-functions">Report plotting functions</a></li>
<li><a class="reference internal" href="#utility-functions">Utility functions</a></li>
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