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<h1>0.9.0<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h1>
<p><strong>Released January 2022</strong></p>
<div class="section" id="highlights">
<h2>HIGHLIGHTS<a class="headerlink" href="#highlights" title="Permalink to this headline">¶</a></h2>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<div class="line-block">
<div class="line"><strong>Python 3.6 is deprecated and will be removed in release 0.10.</strong></div>
<div class="line"><strong>We recommend upgrading to Python 3.9.</strong></div>
<div class="line"><br /></div>
<div class="line"><strong>Nibabel 2.x is no longer supported. Please consider upgrading to Nibabel >= 3.0.</strong></div>
<div class="line"><br /></div>
<div class="line"><strong>Minimum supported versions of packages have been bumped up:</strong></div>
<div class="line">- Numpy – v1.18</div>
<div class="line">- SciPy – v1.5</div>
<div class="line">- Scikit-learn – v0.22</div>
<div class="line">- Pandas – v1.0</div>
<div class="line">- Joblib – v0.15</div>
</div>
</div>
<ul class="simple">
<li><p>Surface plotting functions can now produce interactive plots with <code class="docutils literal notranslate"><span class="pre">Plotly</span></code>. This can be selected with the <code class="docutils literal notranslate"><span class="pre">engine</span></code> parameter (set it to <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code> or <code class="docutils literal notranslate"><span class="pre">plotly</span></code>) (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2902">#2902</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>New module <a class="reference internal" href="../modules/reference.html#module-nilearn.interfaces" title="nilearn.interfaces"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.interfaces</span></code></a> to implement loading and saving utilities with various interfaces (<a class="reference internal" href="../glossary.html#term-fMRIPrep"><span class="xref std std-term">fMRIPrep</span></a>, <a class="reference internal" href="../glossary.html#term-BIDS"><span class="xref std std-term">BIDS</span></a>…) (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3061">#3061</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>New functions <a class="reference internal" href="../modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds" title="nilearn.interfaces.fmriprep.load_confounds"><code class="xref py py-func docutils literal notranslate"><span class="pre">load_confounds</span></code></a> and <a class="reference internal" href="../modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html#nilearn.interfaces.fmriprep.load_confounds_strategy" title="nilearn.interfaces.fmriprep.load_confounds_strategy"><code class="xref py py-func docutils literal notranslate"><span class="pre">load_confounds_strategy</span></code></a> to load confound variables easily from <a class="reference internal" href="../glossary.html#term-fMRIPrep"><span class="xref std std-term">fMRIPrep</span></a> outputs (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2946">#2946</a> and <a class="reference external" href="https://github.com/nilearn/nilearn/issues/3016">#3016</a> by <a class="reference external" href="https://wanghaoting.com/">Hao-Ting Wang</a>).</p></li>
<li><p>New class <a class="reference internal" href="../modules/generated/nilearn.regions.HierarchicalKMeans.html#nilearn.regions.HierarchicalKMeans" title="nilearn.regions.HierarchicalKMeans"><code class="xref py py-class docutils literal notranslate"><span class="pre">HierarchicalKMeans</span></code></a> which yields more balanced clusters than <a class="reference external" href="https://scikit-learn.org/stable/modules/generated/sklearn.cluster.KMeans.html#sklearn.cluster.KMeans" title="(in scikit-learn v1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">KMeans</span></code></a>. It is also callable through <a class="reference internal" href="../modules/generated/nilearn.regions.Parcellations.html#nilearn.regions.Parcellations" title="nilearn.regions.Parcellations"><code class="xref py py-class docutils literal notranslate"><span class="pre">Parcellations</span></code></a> using <code class="docutils literal notranslate"><span class="pre">method=hierarchical_kmeans</span></code> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2282">#2282</a> by <a class="reference external" href="https://github.com/thomasbazeille">Thomas Bazeille</a>).</p></li>
<li><p>Masker objects like <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker" title="nilearn.maskers.NiftiMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiMasker</span></code></a> now belong to the new module <a class="reference internal" href="../modules/reference.html#module-nilearn.maskers" title="nilearn.maskers"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.maskers</span></code></a>. The old import style, through the module <code class="docutils literal notranslate"><span class="pre">input_data</span></code>, still works but has been deprecated (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3065">#3065</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Class <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMapsMasker.html#nilearn.maskers.NiftiMapsMasker" title="nilearn.maskers.NiftiMapsMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiMapsMasker</span></code></a> can now generate HTML reports in the same way as <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker" title="nilearn.maskers.NiftiMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiMasker</span></code></a> and <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiLabelsMasker.html#nilearn.maskers.NiftiLabelsMasker" title="nilearn.maskers.NiftiLabelsMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiLabelsMasker</span></code></a> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2880">#2880</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>The <a class="reference internal" href="../development.html"><span class="doc">contributing documentation</span></a> and <a class="reference internal" href="../maintenance.html"><span class="doc">maintenance</span></a> pages were improved (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3010">#3010</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
</ul>
</div>
<div class="section" id="new">
<h2>NEW<a class="headerlink" href="#new" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p><strong>Support for Python 3.6 is deprecated and will be removed in release 0.10.</strong> Users with a Python 3.6 environment will be warned at their first Nilearn import and encouraged to update to more recent versions of Python (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3026">#3026</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Masker objects like <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker" title="nilearn.maskers.NiftiMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiMasker</span></code></a> now belong to the new module <a class="reference internal" href="../modules/reference.html#module-nilearn.maskers" title="nilearn.maskers"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.maskers</span></code></a>. The old import style, through the module <code class="docutils literal notranslate"><span class="pre">input_data</span></code>, still works but has been deprecated (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3065">#3065</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>New module <a class="reference internal" href="../modules/reference.html#module-nilearn.interfaces" title="nilearn.interfaces"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.interfaces</span></code></a> to implement loading and saving utilities with various interfaces (<a class="reference internal" href="../glossary.html#term-fMRIPrep"><span class="xref std std-term">fMRIPrep</span></a>, <a class="reference internal" href="../glossary.html#term-BIDS"><span class="xref std std-term">BIDS</span></a>…) (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3061">#3061</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>New submodule <a class="reference internal" href="../modules/reference.html#module-nilearn.interfaces.fmriprep" title="nilearn.interfaces.fmriprep"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.interfaces.fmriprep</span></code></a> to implement loading utilities for <a class="reference internal" href="../glossary.html#term-fMRIPrep"><span class="xref std std-term">fMRIPrep</span></a> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3061">#3061</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>New function <a class="reference internal" href="../modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds" title="nilearn.interfaces.fmriprep.load_confounds"><code class="xref py py-func docutils literal notranslate"><span class="pre">load_confounds</span></code></a> to load confound variables easily from <a class="reference internal" href="../glossary.html#term-fMRIPrep"><span class="xref std std-term">fMRIPrep</span></a> outputs (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2946">#2946</a> by <a class="reference external" href="https://wanghaoting.com/">Hao-Ting Wang</a>).</p></li>
<li><p>New function <a class="reference internal" href="../modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html#nilearn.interfaces.fmriprep.load_confounds_strategy" title="nilearn.interfaces.fmriprep.load_confounds_strategy"><code class="xref py py-func docutils literal notranslate"><span class="pre">load_confounds_strategy</span></code></a> to load confound variables from <a class="reference internal" href="../glossary.html#term-fMRIPrep"><span class="xref std std-term">fMRIPrep</span></a> outputs using four preset strategies: <code class="docutils literal notranslate"><span class="pre">simple</span></code>, <code class="docutils literal notranslate"><span class="pre">scrubbing</span></code>, <code class="docutils literal notranslate"><span class="pre">compcor</span></code>, and <code class="docutils literal notranslate"><span class="pre">ica_aroma</span></code> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3016">#3016</a> by <a class="reference external" href="https://wanghaoting.com/">Hao-Ting Wang</a>).</p></li>
<li><p>New submodule <a class="reference internal" href="../modules/reference.html#module-nilearn.interfaces.bids" title="nilearn.interfaces.bids"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.interfaces.bids</span></code></a> to implement loading utilities for <a class="reference internal" href="../glossary.html#term-BIDS"><span class="xref std std-term">BIDS</span></a> datasets (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3126">#3126</a> by <a class="reference external" href="https://tsalo.github.io/">Taylor Salo</a>).</p></li>
<li><p>New function <a class="reference internal" href="../modules/generated/nilearn.interfaces.bids.get_bids_files.html#nilearn.interfaces.bids.get_bids_files" title="nilearn.interfaces.bids.get_bids_files"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_bids_files</span></code></a> to select files easily from <a class="reference internal" href="../glossary.html#term-BIDS"><span class="xref std std-term">BIDS</span></a> datasets (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3126">#3126</a> by <a class="reference external" href="https://tsalo.github.io/">Taylor Salo</a>).</p></li>
<li><p>New function <a class="reference internal" href="../modules/generated/nilearn.interfaces.bids.parse_bids_filename.html#nilearn.interfaces.bids.parse_bids_filename" title="nilearn.interfaces.bids.parse_bids_filename"><code class="xref py py-func docutils literal notranslate"><span class="pre">parse_bids_filename</span></code></a> to identify subparts of <a class="reference internal" href="../glossary.html#term-BIDS"><span class="xref std std-term">BIDS</span></a> filenames (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3126">#3126</a> by <a class="reference external" href="https://tsalo.github.io/">Taylor Salo</a>).</p></li>
<li><p>New submodule <a class="reference internal" href="../modules/reference.html#module-nilearn.interfaces.fsl" title="nilearn.interfaces.fsl"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.interfaces.fsl</span></code></a> to implement loading utilities for FSL outputs. (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3126">#3126</a> by <a class="reference external" href="https://tsalo.github.io/">Taylor Salo</a>).</p></li>
<li><p>New function <a class="reference internal" href="../modules/generated/nilearn.interfaces.fsl.get_design_from_fslmat.html#nilearn.interfaces.fsl.get_design_from_fslmat" title="nilearn.interfaces.fsl.get_design_from_fslmat"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_design_from_fslmat</span></code></a> to load design matrices from FSL files (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3126">#3126</a> by <a class="reference external" href="https://tsalo.github.io/">Taylor Salo</a>).</p></li>
<li><p>Surface plotting functions like <a class="reference internal" href="../modules/generated/nilearn.plotting.plot_surf_stat_map.html#nilearn.plotting.plot_surf_stat_map" title="nilearn.plotting.plot_surf_stat_map"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot_surf_stat_map</span></code></a> now have an <code class="docutils literal notranslate"><span class="pre">engine</span></code> parameter, defaulting to <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code>, but which can be set to <code class="docutils literal notranslate"><span class="pre">plotly</span></code>. If <code class="docutils literal notranslate"><span class="pre">plotly</span></code> and <code class="docutils literal notranslate"><span class="pre">kaleido</span></code> are installed, this will generate an interactive plot of the surface map using <code class="docutils literal notranslate"><span class="pre">plotly</span></code> instead of <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code>. Note that this functionality is still experimental, and that some capabilities supported by our <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code> engine are not yet supported by the <code class="docutils literal notranslate"><span class="pre">plotly</span></code> engine (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2902">#2902</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>When using the <code class="docutils literal notranslate"><span class="pre">plotly</span></code> engine, surface plotting functions derived from <a class="reference internal" href="../modules/generated/nilearn.plotting.plot_surf.html#nilearn.plotting.plot_surf" title="nilearn.plotting.plot_surf"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot_surf</span></code></a> return a new display object, a <a class="reference internal" href="../modules/generated/nilearn.plotting.displays.PlotlySurfaceFigure.html#nilearn.plotting.displays.PlotlySurfaceFigure" title="nilearn.plotting.displays.PlotlySurfaceFigure"><code class="xref py py-class docutils literal notranslate"><span class="pre">PlotlySurfaceFigure</span></code></a>, which provides a similar interface to the <a class="reference external" href="https://matplotlib.org/stable/api/figure_api.html#matplotlib.figure.Figure" title="(in Matplotlib v3.5.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Figure</span></code></a> returned with the <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code> engine (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3036">#3036</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Class <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMapsMasker.html#nilearn.maskers.NiftiMapsMasker" title="nilearn.maskers.NiftiMapsMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiMapsMasker</span></code></a> can now generate HTML reports in the same way as <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker" title="nilearn.maskers.NiftiMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiMasker</span></code></a> and <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiLabelsMasker.html#nilearn.maskers.NiftiLabelsMasker" title="nilearn.maskers.NiftiLabelsMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiLabelsMasker</span></code></a>. The report enables the users to browse through the spatial maps with a previous and next button. The users can filter the maps they wish to display by passing an integer, or a list of integers to <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMapsMasker.html#nilearn.maskers.NiftiMapsMasker.generate_report" title="nilearn.maskers.NiftiMapsMasker.generate_report"><code class="xref py py-meth docutils literal notranslate"><span class="pre">generate_report</span></code></a> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2880">#2880</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>New class <a class="reference internal" href="../modules/generated/nilearn.regions.HierarchicalKMeans.html#nilearn.regions.HierarchicalKMeans" title="nilearn.regions.HierarchicalKMeans"><code class="xref py py-class docutils literal notranslate"><span class="pre">HierarchicalKMeans</span></code></a> which yields more balanced clusters than <a class="reference external" href="https://scikit-learn.org/stable/modules/generated/sklearn.cluster.KMeans.html#sklearn.cluster.KMeans" title="(in scikit-learn v1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">KMeans</span></code></a>. It is also callable through <a class="reference internal" href="../modules/generated/nilearn.regions.Parcellations.html#nilearn.regions.Parcellations" title="nilearn.regions.Parcellations"><code class="xref py py-class docutils literal notranslate"><span class="pre">Parcellations</span></code></a> using <code class="docutils literal notranslate"><span class="pre">method=hierarchical_kmeans</span></code> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2282">#2282</a> by <a class="reference external" href="https://github.com/thomasbazeille">Thomas Bazeille</a>).</p></li>
</ul>
</div>
<div class="section" id="fixes">
<h2>Fixes<a class="headerlink" href="#fixes" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>When a label image with non integer values was provided to the <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiLabelsMasker.html#nilearn.maskers.NiftiLabelsMasker" title="nilearn.maskers.NiftiLabelsMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiLabelsMasker</span></code></a>, its <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiLabelsMasker.html#nilearn.maskers.NiftiLabelsMasker.generate_report" title="nilearn.maskers.NiftiLabelsMasker.generate_report"><code class="xref py py-meth docutils literal notranslate"><span class="pre">generate_report</span></code></a> method was raising an <code class="docutils literal notranslate"><span class="pre">IndexError</span></code> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3009">#3009</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Function <a class="reference internal" href="../modules/generated/nilearn.plotting.plot_markers.html#nilearn.plotting.plot_markers" title="nilearn.plotting.plot_markers"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot_markers</span></code></a> did not work when the <code class="docutils literal notranslate"><span class="pre">display_mode</span></code> parameter included <code class="docutils literal notranslate"><span class="pre">l</span></code> and <code class="docutils literal notranslate"><span class="pre">r</span></code> and the parameter <code class="docutils literal notranslate"><span class="pre">node_size</span></code> was provided as an array (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3013">#3013</a> by <a class="reference external" href="https://github.com/LeSasse">Leonard Sasse</a>).</p></li>
<li><p>Method <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.FirstLevelModel.html#nilearn.glm.first_level.FirstLevelModel.generate_report" title="nilearn.glm.first_level.FirstLevelModel.generate_report"><code class="xref py py-meth docutils literal notranslate"><span class="pre">generate_report</span></code></a> threw a <code class="docutils literal notranslate"><span class="pre">TypeError</span></code> when <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.FirstLevelModel.html#nilearn.glm.first_level.FirstLevelModel" title="nilearn.glm.first_level.FirstLevelModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">FirstLevelModel</span></code></a> was instantiated with <code class="docutils literal notranslate"><span class="pre">mask_img</span></code> being a <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker" title="nilearn.maskers.NiftiMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiMasker</span></code></a>. Function <a class="reference internal" href="../modules/generated/nilearn.reporting.make_glm_report.html#nilearn.reporting.make_glm_report" title="nilearn.reporting.make_glm_report"><code class="xref py py-func docutils literal notranslate"><span class="pre">make_glm_report</span></code></a> was fixed accordingly (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3035">#3035</a> by <a class="reference external" href="https://github.com/alexisthual">Alexis Thual</a>).</p></li>
<li><p>Function <a class="reference internal" href="../modules/generated/nilearn.plotting.find_parcellation_cut_coords.html#nilearn.plotting.find_parcellation_cut_coords" title="nilearn.plotting.find_parcellation_cut_coords"><code class="xref py py-func docutils literal notranslate"><span class="pre">find_parcellation_cut_coords</span></code></a> now returns coordinates and labels having the same order as the one of the input labels index (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3078">#3078</a> by <a class="reference external" href="https://github.com/NeuroVR-Song">Myeong Seop Song</a>).</p></li>
<li><p>Convert references in <code class="docutils literal notranslate"><span class="pre">nilearn/regions/region_extractor.py</span></code> to use footcite / footbibliography (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3111">#3111</a> by <a class="reference external" href="https://github.com/NeelayS">Neelay Shah</a>).</p></li>
<li><p>Fixed Hommel value computation in <code class="docutils literal notranslate"><span class="pre">nilearn/glm/thresholding.py</span></code> used in the <code class="docutils literal notranslate"><span class="pre">cluster_level_inference</span></code> function (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3109">#3109</a> by <a class="reference external" href="https://pages.saclay.inria.fr/bertrand.thirion/">Bertrand Thirion</a>).</p></li>
<li><p>Fixed computation of Benjamini-Hocheberg threshold in <code class="docutils literal notranslate"><span class="pre">nilearn/glm/thresholding.py</span></code> function (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3137">#3137</a> by <a class="reference external" href="https://pages.saclay.inria.fr/bertrand.thirion/">Bertrand Thirion</a>).</p></li>
<li><p>Attribute <code class="docutils literal notranslate"><span class="pre">scaling_axis</span></code> of <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.FirstLevelModel.html#nilearn.glm.first_level.FirstLevelModel" title="nilearn.glm.first_level.FirstLevelModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">FirstLevelModel</span></code></a> has been deprecated and will be removed in <code class="docutils literal notranslate"><span class="pre">0.11.0</span></code>. When scaling is performed, the attribute <code class="docutils literal notranslate"><span class="pre">signal_scaling</span></code> is used to define the axis instead (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3135">#3135</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
</ul>
</div>
<div class="section" id="enhancements">
<h2>Enhancements<a class="headerlink" href="#enhancements" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>Function <a class="reference internal" href="../modules/generated/nilearn.image.threshold_img.html#nilearn.image.threshold_img" title="nilearn.image.threshold_img"><code class="xref py py-func docutils literal notranslate"><span class="pre">threshold_img</span></code></a> accepts new parameters <code class="docutils literal notranslate"><span class="pre">cluster_threshold</span></code> and <code class="docutils literal notranslate"><span class="pre">two_sided</span></code>. <code class="docutils literal notranslate"><span class="pre">cluster_threshold</span></code> applies a cluster-size threshold (in <a class="reference internal" href="../glossary.html#term-voxel"><span class="xref std std-term">voxels</span></a>). <code class="docutils literal notranslate"><span class="pre">two_sided</span></code>, which is <code class="docutils literal notranslate"><span class="pre">True</span></code> by default, separately thresholds both positive and negative values in the map, as was done previously. When <code class="docutils literal notranslate"><span class="pre">two_sided</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>, only values greater than or equal to the threshold are retained (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2965">#2965</a> by <a class="reference external" href="https://tsalo.github.io/">Taylor Salo</a>).</p></li>
<li><p>Function <a class="reference internal" href="../modules/generated/nilearn.signal.clean.html#nilearn.signal.clean" title="nilearn.signal.clean"><code class="xref py py-func docutils literal notranslate"><span class="pre">clean</span></code></a> raises a warning when the user sets parameters <code class="docutils literal notranslate"><span class="pre">detrend</span></code> and <code class="docutils literal notranslate"><span class="pre">standardize_confound</span></code> to <code class="docutils literal notranslate"><span class="pre">False</span></code>. The user is suggested to set one of those options to <code class="docutils literal notranslate"><span class="pre">True</span></code>, or standardize/demean the confounds before using the function (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3003">#3003</a> by <a class="reference external" href="https://wanghaoting.com/">Hao-Ting Wang</a>).</p></li>
<li><p>The <a class="reference internal" href="../development.html"><span class="doc">contributing documentation</span></a> and <a class="reference internal" href="../maintenance.html"><span class="doc">maintenance</span></a> pages were improved, especially towards ways of contributing to the project which do not require to write code. The roles of the <a class="reference internal" href="../authors.html#triage"><span class="std std-ref">Triage team</span></a> were defined more clearly with sections on issue <a class="reference internal" href="../maintenance.html#issue-labels"><span class="std std-ref">Labels</span></a> and issue <a class="reference internal" href="../maintenance.html#closing-policy"><span class="std std-ref">Closing policy</span></a> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3010">#3010</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>It is now possible to provide custom <a class="reference internal" href="../glossary.html#term-HRF"><span class="xref std std-term">HRF</span></a> models to <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.FirstLevelModel.html#nilearn.glm.first_level.FirstLevelModel" title="nilearn.glm.first_level.FirstLevelModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">FirstLevelModel</span></code></a>. The custom model should be defined as a function, or a list of functions, implementing the same API as Nilearn’s usual models (see <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.spm_hrf.html#nilearn.glm.first_level.spm_hrf" title="nilearn.glm.first_level.spm_hrf"><code class="xref py py-func docutils literal notranslate"><span class="pre">spm_hrf</span></code></a> for example). The example <a class="reference internal" href="../auto_examples/04_glm_first_level/plot_hrf.html#sphx-glr-auto-examples-04-glm-first-level-plot-hrf-py"><span class="std std-ref">Example of MRI response functions</span></a> was also modified to demo how to define custom <a class="reference internal" href="../glossary.html#term-HRF"><span class="xref std std-term">HRF</span></a> models (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2942">#2942</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Class <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiLabelsMasker.html#nilearn.maskers.NiftiLabelsMasker" title="nilearn.maskers.NiftiLabelsMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiLabelsMasker</span></code></a> now gives a warning when some labels are removed from the label image at transform time due to resampling of the label image to the data image (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3008">#3008</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Function <a class="reference internal" href="../modules/generated/nilearn.glm.second_level.non_parametric_inference.html#nilearn.glm.second_level.non_parametric_inference" title="nilearn.glm.second_level.non_parametric_inference"><code class="xref py py-func docutils literal notranslate"><span class="pre">non_parametric_inference</span></code></a> now accepts <a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v1.4.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">DataFrame</span></code></a> as possible values for its <code class="docutils literal notranslate"><span class="pre">second_level_input</span></code> parameter. Note that a new parameter <code class="docutils literal notranslate"><span class="pre">first_level_contrast</span></code> has been added to this function to enable this feature (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3042">#3042</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Tests from <code class="docutils literal notranslate"><span class="pre">nilearn/plotting/tests/test_img_plotting.py</span></code> have been refactored and reorganized in separate files in new folder <code class="docutils literal notranslate"><span class="pre">nilearn/plotting/tests/test_img_plotting/</span></code> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3015">#3015</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Once a <a class="reference internal" href="../modules/generated/nilearn.glm.second_level.SecondLevelModel.html#nilearn.glm.second_level.SecondLevelModel" title="nilearn.glm.second_level.SecondLevelModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">SecondLevelModel</span></code></a> has been fitted and contrasts have been computed, it is now possible to access the <code class="docutils literal notranslate"><span class="pre">residuals</span></code>, <code class="docutils literal notranslate"><span class="pre">predicted</span></code>, and <code class="docutils literal notranslate"><span class="pre">r_square</span></code> model attributes like it was already possible for <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.FirstLevelModel.html#nilearn.glm.first_level.FirstLevelModel" title="nilearn.glm.first_level.FirstLevelModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">FirstLevelModel</span></code></a> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3033">#3033</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Importing <a class="reference internal" href="../modules/reference.html#module-nilearn.plotting" title="nilearn.plotting"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.plotting</span></code></a> will now raise a warning if the <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code> backend has been changed from its original value, instead of silently modifying it (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3077">#3077</a> by <a class="reference external" href="https://github.com/RaphaelMeudec">Raphael Meudec</a>).</p></li>
<li><p>Function <a class="reference internal" href="../modules/generated/nilearn.plotting.plot_img.html#nilearn.plotting.plot_img" title="nilearn.plotting.plot_img"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot_img</span></code></a> and deriving functions like <a class="reference internal" href="../modules/generated/nilearn.plotting.plot_anat.html#nilearn.plotting.plot_anat" title="nilearn.plotting.plot_anat"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot_anat</span></code></a>, <a class="reference internal" href="../modules/generated/nilearn.plotting.plot_stat_map.html#nilearn.plotting.plot_stat_map" title="nilearn.plotting.plot_stat_map"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot_stat_map</span></code></a>, or <a class="reference internal" href="../modules/generated/nilearn.plotting.plot_epi.html#nilearn.plotting.plot_epi" title="nilearn.plotting.plot_epi"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot_epi</span></code></a> now accept an optional argument <code class="docutils literal notranslate"><span class="pre">cbar_tick_format</span></code> to specify how numbers should be displayed on the colorbar. This is consistent with the API of surface plotting functions (see release <code class="docutils literal notranslate"><span class="pre">0.7.1</span></code>). The default format is scientific notation (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2859">#2859</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
</ul>
</div>
<div class="section" id="changes">
<h2>Changes<a class="headerlink" href="#changes" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>Nibabel 2.x is no longer supported. Please consider upgrading to Nibabel >= 3.0 (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3106">#3106</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Deprecated function <code class="docutils literal notranslate"><span class="pre">nilearn.datasets.fetch_cobre</span></code> has been removed (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3081">#3081</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Deprecated function <code class="docutils literal notranslate"><span class="pre">nilearn.plotting.plot_connectome_strength</span></code> has been removed (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3082">#3082</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Deprecated function <code class="docutils literal notranslate"><span class="pre">nilearn.masking.compute_gray_matter_mask</span></code> has been removed (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3090">#3090</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Deprecated parameter <code class="docutils literal notranslate"><span class="pre">sessions</span></code> of function <a class="reference internal" href="../modules/generated/nilearn.signal.clean.html#nilearn.signal.clean" title="nilearn.signal.clean"><code class="xref py py-func docutils literal notranslate"><span class="pre">clean</span></code></a> has been removed. Use <code class="docutils literal notranslate"><span class="pre">runs</span></code> instead (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3093">#3093</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Deprecated parameters <code class="docutils literal notranslate"><span class="pre">sessions</span></code> and <code class="docutils literal notranslate"><span class="pre">sample_mask</span></code> of <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker" title="nilearn.maskers.NiftiMasker"><code class="xref py py-class docutils literal notranslate"><span class="pre">NiftiMasker</span></code></a> have been removed. Please use <code class="docutils literal notranslate"><span class="pre">runs</span></code> instead of <code class="docutils literal notranslate"><span class="pre">sessions</span></code>, and provide a <code class="docutils literal notranslate"><span class="pre">sample_mask</span></code> through <a class="reference internal" href="../modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker.transform" title="nilearn.maskers.NiftiMasker.transform"><code class="xref py py-meth docutils literal notranslate"><span class="pre">transform</span></code></a> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3133">#3133</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Function <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.compute_regressor.html#nilearn.glm.first_level.compute_regressor" title="nilearn.glm.first_level.compute_regressor"><code class="xref py py-func docutils literal notranslate"><span class="pre">glm.first_level.compute_regressor</span></code></a> will now raise an exception if parameter <code class="docutils literal notranslate"><span class="pre">cond_id</span></code> is not a string which could be used to name a python variable. For instance, number strings (ex: “1”) will no longer be accepted as valid condition names. In particular, this will also impact <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.make_first_level_design_matrix.html#nilearn.glm.first_level.make_first_level_design_matrix" title="nilearn.glm.first_level.make_first_level_design_matrix"><code class="xref py py-func docutils literal notranslate"><span class="pre">glm.first_level.make_first_level_design_matrix</span></code></a> and <a class="reference internal" href="../modules/generated/nilearn.glm.first_level.FirstLevelModel.html#nilearn.glm.first_level.FirstLevelModel" title="nilearn.glm.first_level.FirstLevelModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">glm.first_level.FirstLevelModel</span></code></a>, for which proper condition names will also be needed (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3025">#3025</a> by <a class="reference external" href="https://github.com/alexisthual">Alexis Thual</a>).</p></li>
<li><p>Replace parameter <code class="docutils literal notranslate"><span class="pre">sessions</span></code> with <code class="docutils literal notranslate"><span class="pre">runs</span></code> in function <a class="reference internal" href="../modules/generated/nilearn.image.clean_img.html#nilearn.image.clean_img" title="nilearn.image.clean_img"><code class="xref py py-func docutils literal notranslate"><span class="pre">clean_img</span></code></a> as this replacement was already made for function <a class="reference internal" href="../modules/generated/nilearn.signal.clean.html#nilearn.signal.clean" title="nilearn.signal.clean"><code class="xref py py-func docutils literal notranslate"><span class="pre">clean</span></code></a> in <a class="reference external" href="https://github.com/nilearn/nilearn/issues/2821">#2821</a> in order to match <a class="reference internal" href="../glossary.html#term-BIDS"><span class="xref std std-term">BIDS</span></a> semantics. The use of <code class="docutils literal notranslate"><span class="pre">sessions</span></code> in function <a class="reference internal" href="../modules/generated/nilearn.image.clean_img.html#nilearn.image.clean_img" title="nilearn.image.clean_img"><code class="xref py py-func docutils literal notranslate"><span class="pre">clean_img</span></code></a> is deprecated and will be removed in <code class="docutils literal notranslate"><span class="pre">0.10.0</span></code> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3039">#3039</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Display objects have been reorganized. For example, <code class="docutils literal notranslate"><span class="pre">Slicers</span></code> (like the <a class="reference internal" href="../modules/generated/nilearn.plotting.displays.OrthoSlicer.html#nilearn.plotting.displays.OrthoSlicer" title="nilearn.plotting.displays.OrthoSlicer"><code class="xref py py-class docutils literal notranslate"><span class="pre">OrthoSlicer</span></code></a>) are all in file <code class="docutils literal notranslate"><span class="pre">nilearn/plotting/displays/_slicers.py</span></code>, and <code class="docutils literal notranslate"><span class="pre">Projectors</span></code> (like the <a class="reference internal" href="../modules/generated/nilearn.plotting.displays.OrthoProjector.html#nilearn.plotting.displays.OrthoProjector" title="nilearn.plotting.displays.OrthoProjector"><code class="xref py py-class docutils literal notranslate"><span class="pre">OrthoProjector</span></code></a>) are all in file <code class="docutils literal notranslate"><span class="pre">nilearn/plotting/displays/_projectors.py</span></code>. All display objects have been added to the public API, and examples have been improved to show how to use these objects to customize figures obtained with plotting functions (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/3073">#3073</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Descriptions of datasets retrieved with fetchers from <a class="reference internal" href="../modules/reference.html#module-nilearn.datasets" title="nilearn.datasets"><code class="xref py py-mod docutils literal notranslate"><span class="pre">nilearn.datasets</span></code></a> are now python strings rather than <code class="docutils literal notranslate"><span class="pre">bytes</span></code>. Therefore, decoding the descriptions is no longer necessary (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2655">#2655</a> by <a class="reference external" href="https://nicolasgensollen.github.io/">Nicolas Gensollen</a>).</p></li>
<li><p>Dataset fetchers returning a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.22)"><code class="xref py py-class docutils literal notranslate"><span class="pre">recarray</span></code></a> can now return a <a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v1.4.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">DataFrame</span></code></a> instead. These fetchers now have a <code class="docutils literal notranslate"><span class="pre">legacy_format</span></code> optional argument defaulting to <code class="docutils literal notranslate"><span class="pre">True</span></code> for backward compatibility. Users will be warned that this parameter will default to <code class="docutils literal notranslate"><span class="pre">False</span></code> in release <code class="docutils literal notranslate"><span class="pre">0.11.0</span></code>, making <a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v1.4.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">DataFrame</span></code></a> the default return type instead or <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.22)"><code class="xref py py-class docutils literal notranslate"><span class="pre">recarray</span></code></a> (<a class="reference external" href="https://github.com/nilearn/nilearn/issues/2829">#2829</a> by <a class="reference external" href="https://github.com/achamma723">Ahmad Chamma</a>).</p></li>
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<h4> Giving credit </h4>
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<li><p>Please consider <a href="../authors.html#citing">citing the
papers</a>.</p></li>
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<h3><a href="../index.html">Table of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">0.9.0</a><ul>
<li><a class="reference internal" href="#highlights">HIGHLIGHTS</a></li>
<li><a class="reference internal" href="#new">NEW</a></li>
<li><a class="reference internal" href="#fixes">Fixes</a></li>
<li><a class="reference internal" href="#enhancements">Enhancements</a></li>
<li><a class="reference internal" href="#changes">Changes</a></li>
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