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<ul>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">1. Introduction: fmralign in a nutshell</a><ul>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#functional-alignment-handling-functional-variability">1.1. Functional alignment: handling functional variability</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#installing-fmralign">1.2. Installing fmralign</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="functional_alignment/index.html">2. Functional alignment: handling functional variability</a><ul>
<li class="toctree-l2"><a class="reference internal" href="functional_alignment/functional_alignment_intro.html">2.1. An introduction to functional alignment</a><ul>
<li class="toctree-l3"><a class="reference internal" href="functional_alignment/functional_alignment_intro.html#inter-subject-variability-in-fmri">2.1.1. Inter subject variability in fMRI</a><ul>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/functional_alignment_intro.html#loading-and-preparing-the-data">2.1.1.1. Loading and preparing the data</a></li>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/functional_alignment_intro.html#measure-correlation-between-subjects-images">2.1.1.2. Measure correlation between subjects images</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="functional_alignment/functional_alignment_intro.html#functional-alignment">2.1.2. Functional alignment</a><ul>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/functional_alignment_intro.html#learning-the-transformation-and-predicting-new-data">2.1.2.1. Learning the transformation and predicting new data</a></li>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/functional_alignment_intro.html#measuring-similarity-after-alignment">2.1.2.2. Measuring similarity after alignment</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html">2.2. Functional alignment pipeline</a><ul>
<li class="toctree-l3"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#local-functional-alignment">2.2.1. Local functional alignment</a></li>
<li class="toctree-l3"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#alignment-methods-on-a-region">2.2.2. Alignment methods on a region</a><ul>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#orthogonal-alignment-procrustes">2.2.2.1. Orthogonal alignment (Procrustes)</a></li>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#ridge-alignment">2.2.2.2. Ridge alignment</a></li>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#optimal-transport-alignment">2.2.2.3. Optimal Transport alignment</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#comparing-those-methods-on-a-region-of-interest">2.2.3. Comparing those methods on a region of interest</a><ul>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#loading-the-data">2.2.3.1. Loading the data</a></li>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#extract-a-mask-for-the-visual-cortex-from-yeo-atlas">2.2.3.2. Extract a mask for the visual cortex from Yeo Atlas</a></li>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#define-a-masker">2.2.3.3. Define a masker</a></li>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#prepare-the-data">2.2.3.4. Prepare the data</a></li>
<li class="toctree-l4"><a class="reference internal" href="functional_alignment/fmralign_pipeline.html#define-the-estimators-fit-them-and-do-a-prediction">2.2.3.5. Define the estimators, fit them and do a prediction</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="modules/reference.html">3. Reference documentation: all fmralign functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-fmralign.pairwise_alignment">3.1. <code class="xref py py-mod docutils literal notranslate"><span class="pre">fmralign.pairwise_alignment</span></code>: Pairwise Alignment</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/fmralign.pairwise_alignment.PairwiseAlignment.html">3.1.1. fmralign.pairwise_alignment.PairwiseAlignment</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-fmralign.template_alignment">3.2. <code class="xref py py-mod docutils literal notranslate"><span class="pre">fmralign.template_alignment</span></code>: Template Alignment</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/fmralign.template_alignment.TemplateAlignment.html">3.2.1. fmralign.template_alignment.TemplateAlignment</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/reference.html#module-fmralign.alignment_methods">3.3. <code class="xref py py-mod docutils literal notranslate"><span class="pre">fmralign.alignment_methods</span></code>: Alignment Methods</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/fmralign.alignment_methods.Identity.html">3.3.1. fmralign.alignment_methods.Identity</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/fmralign.alignment_methods.DiagonalAlignment.html">3.3.2. fmralign.alignment_methods.DiagonalAlignment</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/fmralign.alignment_methods.ScaledOrthogonalAlignment.html">3.3.3. fmralign.alignment_methods.ScaledOrthogonalAlignment</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/fmralign.alignment_methods.RidgeAlignment.html">3.3.4. fmralign.alignment_methods.RidgeAlignment</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/fmralign.alignment_methods.Hungarian.html">3.3.5. fmralign.alignment_methods.Hungarian</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/fmralign.alignment_methods.OptimalTransportAlignment.html">3.3.6. fmralign.alignment_methods.OptimalTransportAlignment</a></li>
</ul>
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