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Author: mvdoc

_sources/index.rst.txt

@@ -7,7 +7,7 @@ Welcome to the voxelwise modeling tutorials from the
 
 If you use these tutorials for your work, consider citing the corresponding paper:
 
-Dupré La Tour, T., Visconti di Oleggio Castello, M., & Gallant, J. L. (2024). The Voxelwise Modeling framework: a tutorial introduction to fitting encoding models to fMRI data.
+Dupré la Tour, T., Visconti di Oleggio Castello, M., & Gallant, J. L. (2024). The Voxelwise Modeling framework: a tutorial introduction to fitting encoding models to fMRI data. https://doi.org/10.31234/osf.io/t975e
 
 You can find a copy of the paper `here <https://github.com/gallantlab/voxelwise_tutorials/blob/main/paper/voxelwise_tutorials_paper.pdf>`_.
 

_sources/references.rst.txt

@@ -128,7 +128,7 @@ Packages
 
 [p1] Dupré La Tour, T., Visconti di Oleggio Castello, M., & Gallant, J. L. (2024).
    The Voxelwise Modeling framework: a tutorial introduction to fitting encoding models to fMRI data.
-   *Under review*.
+   https://doi.org/10.31234/osf.io/t975e
 
 [p2] Dupré La Tour, T., Eickenberg, M., Nunez-Elizalde, A.O., & Gallant, J. L. (2022).
     Feature-space selection with banded ridge regression.

_sources/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**12:58.385** total execution time for 12 files **from all galleries**:
+**00:00.000** total execution time for 12 files **from all galleries**:
 
 .. container::
 
@@ -32,31 +32,28 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
-   * - :ref:`sphx_glr__auto_examples_vim2_02_plot_ridge_model.py` (``../tutorials/vim2/02_plot_ridge_model.py``)
-     - 07:12.384
-     - 0.0
-   * - :ref:`sphx_glr__auto_examples_shortclips_06_plot_banded_ridge_model.py` (``../tutorials/shortclips/06_plot_banded_ridge_model.py``)
-     - 01:58.143
-     - 0.0
-   * - :ref:`sphx_glr__auto_examples_shortclips_03_plot_wordnet_model.py` (``../tutorials/shortclips/03_plot_wordnet_model.py``)
-     - 01:16.347
-     - 0.0
-   * - :ref:`sphx_glr__auto_examples_shortclips_05_plot_motion_energy_model.py` (``../tutorials/shortclips/05_plot_motion_energy_model.py``)
-     - 00:58.974
+   * - :ref:`sphx_glr__auto_examples_shortclips_00_download_shortclips.py` (``../tutorials/shortclips/00_download_shortclips.py``)
+     - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr__auto_examples_shortclips_04_plot_hemodynamic_response.py` (``../tutorials/shortclips/04_plot_hemodynamic_response.py``)
-     - 00:57.648
+   * - :ref:`sphx_glr__auto_examples_shortclips_00_setup_colab.py` (``../tutorials/shortclips/00_setup_colab.py``)
+     - 00:00.000
      - 0.0
    * - :ref:`sphx_glr__auto_examples_shortclips_01_plot_explainable_variance.py` (``../tutorials/shortclips/01_plot_explainable_variance.py``)
-     - 00:28.850
+     - 00:00.000
      - 0.0
    * - :ref:`sphx_glr__auto_examples_shortclips_02_plot_ridge_regression.py` (``../tutorials/shortclips/02_plot_ridge_regression.py``)
-     - 00:06.038
+     - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr__auto_examples_shortclips_00_download_shortclips.py` (``../tutorials/shortclips/00_download_shortclips.py``)
+   * - :ref:`sphx_glr__auto_examples_shortclips_03_plot_wordnet_model.py` (``../tutorials/shortclips/03_plot_wordnet_model.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr__auto_examples_shortclips_00_setup_colab.py` (``../tutorials/shortclips/00_setup_colab.py``)
+   * - :ref:`sphx_glr__auto_examples_shortclips_04_plot_hemodynamic_response.py` (``../tutorials/shortclips/04_plot_hemodynamic_response.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr__auto_examples_shortclips_05_plot_motion_energy_model.py` (``../tutorials/shortclips/05_plot_motion_energy_model.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr__auto_examples_shortclips_06_plot_banded_ridge_model.py` (``../tutorials/shortclips/06_plot_banded_ridge_model.py``)
      - 00:00.000
      - 0.0
    * - :ref:`sphx_glr__auto_examples_shortclips_07_extract_motion_energy.py` (``../tutorials/shortclips/07_extract_motion_energy.py``)
@@ -68,3 +65,6 @@ Computation times
    * - :ref:`sphx_glr__auto_examples_vim2_01_extract_motion_energy.py` (``../tutorials/vim2/01_extract_motion_energy.py``)
      - 00:00.000
      - 0.0
+   * - :ref:`sphx_glr__auto_examples_vim2_02_plot_ridge_model.py` (``../tutorials/vim2/02_plot_ridge_model.py``)
+     - 00:00.000
+     - 0.0

index.html

@@ -97,7 +97,7 @@ <h1>Voxelwise modeling tutorials<a class="headerlink" href="#voxelwise-modeling-
 <p>Welcome to the voxelwise modeling tutorials from the
 <a class="reference external" href="https://gallantlab.org">GallantLab</a>.</p>
 <p>If you use these tutorials for your work, consider citing the corresponding paper:</p>
-<p>Dupré La Tour, T., Visconti di Oleggio Castello, M., &amp; Gallant, J. L. (2024). The Voxelwise Modeling framework: a tutorial introduction to fitting encoding models to fMRI data.</p>
+<p>Dupré la Tour, T., Visconti di Oleggio Castello, M., &amp; Gallant, J. L. (2024). The Voxelwise Modeling framework: a tutorial introduction to fitting encoding models to fMRI data. <a class="reference external" href="https://doi.org/10.31234/osf.io/t975e">https://doi.org/10.31234/osf.io/t975e</a></p>
 <p>You can find a copy of the paper <a class="reference external" href="https://github.com/gallantlab/voxelwise_tutorials/blob/main/paper/voxelwise_tutorials_paper.pdf">here</a>.</p>
 <section id="getting-started">
 <h2>Getting started<a class="headerlink" href="#getting-started" title="Link to this heading">¶</a></h2>

references.html

@@ -199,7 +199,7 @@ <h2>Datasets<a class="headerlink" href="#datasets" title="Link to this heading">
 <h2>Packages<a class="headerlink" href="#packages" title="Link to this heading">¶</a></h2>
 <dl class="simple" id="dup2023">
 <dt>[p1] Dupré La Tour, T., Visconti di Oleggio Castello, M., &amp; Gallant, J. L. (2024).</dt><dd><p>The Voxelwise Modeling framework: a tutorial introduction to fitting encoding models to fMRI data.
-<em>Under review</em>.</p>
+<a class="reference external" href="https://doi.org/10.31234/osf.io/t975e">https://doi.org/10.31234/osf.io/t975e</a></p>
 </dd>
 <dt>[p2] Dupré La Tour, T., Eickenberg, M., Nunez-Elizalde, A.O., &amp; Gallant, J. L. (2022).</dt><dd><p>Feature-space selection with banded ridge regression.
 NeuroImage. <a class="reference external" href="https://doi.org/10.1016/j.neuroimage.2022.119728">https://doi.org/10.1016/j.neuroimage.2022.119728</a></p>

searchindex.js

@@ -92,7 +92,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <section id="computation-times">
 <span id="sphx-glr-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading">¶</a></h1>
-<p><strong>12:58.385</strong> total execution time for 12 files <strong>from all galleries</strong>:</p>
+<p><strong>00:00.000</strong> total execution time for 12 files <strong>from all galleries</strong>:</p>
 <div class="docutils container">
 <style scoped>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
@@ -113,51 +113,51 @@ <h3 id="searchlabel">Quick search</h3>
 </tr>
 </thead>
 <tbody>
-<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/vim2/02_plot_ridge_model.html#sphx-glr-auto-examples-vim2-02-plot-ridge-model-py"><span class="std std-ref">Fit a ridge model with motion energy features</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/vim2/02_plot_ridge_model.py</span></code>)</p></td>
-<td><p>07:12.384</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/00_download_shortclips.html#sphx-glr-auto-examples-shortclips-00-download-shortclips-py"><span class="std std-ref">Download the data set</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/00_download_shortclips.py</span></code>)</p></td>
+<td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/06_plot_banded_ridge_model.html#sphx-glr-auto-examples-shortclips-06-plot-banded-ridge-model-py"><span class="std std-ref">Fit a banded ridge model with both wordnet and motion energy features</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/06_plot_banded_ridge_model.py</span></code>)</p></td>
-<td><p>01:58.143</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/00_setup_colab.html#sphx-glr-auto-examples-shortclips-00-setup-colab-py"><span class="std std-ref">Setup Google Colab</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/00_setup_colab.py</span></code>)</p></td>
+<td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/03_plot_wordnet_model.html#sphx-glr-auto-examples-shortclips-03-plot-wordnet-model-py"><span class="std std-ref">Fit a ridge model with wordnet features</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/03_plot_wordnet_model.py</span></code>)</p></td>
-<td><p>01:16.347</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/01_plot_explainable_variance.html#sphx-glr-auto-examples-shortclips-01-plot-explainable-variance-py"><span class="std std-ref">Compute the explainable variance</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/01_plot_explainable_variance.py</span></code>)</p></td>
+<td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/05_plot_motion_energy_model.html#sphx-glr-auto-examples-shortclips-05-plot-motion-energy-model-py"><span class="std std-ref">Fit a ridge model with motion energy features</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/05_plot_motion_energy_model.py</span></code>)</p></td>
-<td><p>00:58.974</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/02_plot_ridge_regression.html#sphx-glr-auto-examples-shortclips-02-plot-ridge-regression-py"><span class="std std-ref">Understand ridge regression and cross-validation</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/02_plot_ridge_regression.py</span></code>)</p></td>
+<td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/04_plot_hemodynamic_response.html#sphx-glr-auto-examples-shortclips-04-plot-hemodynamic-response-py"><span class="std std-ref">Visualize the hemodynamic response</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/04_plot_hemodynamic_response.py</span></code>)</p></td>
-<td><p>00:57.648</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/03_plot_wordnet_model.html#sphx-glr-auto-examples-shortclips-03-plot-wordnet-model-py"><span class="std std-ref">Fit a ridge model with wordnet features</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/03_plot_wordnet_model.py</span></code>)</p></td>
+<td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/01_plot_explainable_variance.html#sphx-glr-auto-examples-shortclips-01-plot-explainable-variance-py"><span class="std std-ref">Compute the explainable variance</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/01_plot_explainable_variance.py</span></code>)</p></td>
-<td><p>00:28.850</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/04_plot_hemodynamic_response.html#sphx-glr-auto-examples-shortclips-04-plot-hemodynamic-response-py"><span class="std std-ref">Visualize the hemodynamic response</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/04_plot_hemodynamic_response.py</span></code>)</p></td>
+<td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/02_plot_ridge_regression.html#sphx-glr-auto-examples-shortclips-02-plot-ridge-regression-py"><span class="std std-ref">Understand ridge regression and cross-validation</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/02_plot_ridge_regression.py</span></code>)</p></td>
-<td><p>00:06.038</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/05_plot_motion_energy_model.html#sphx-glr-auto-examples-shortclips-05-plot-motion-energy-model-py"><span class="std std-ref">Fit a ridge model with motion energy features</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/05_plot_motion_energy_model.py</span></code>)</p></td>
+<td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/00_download_shortclips.html#sphx-glr-auto-examples-shortclips-00-download-shortclips-py"><span class="std std-ref">Download the data set</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/00_download_shortclips.py</span></code>)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/06_plot_banded_ridge_model.html#sphx-glr-auto-examples-shortclips-06-plot-banded-ridge-model-py"><span class="std std-ref">Fit a banded ridge model with both wordnet and motion energy features</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/06_plot_banded_ridge_model.py</span></code>)</p></td>
 <td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/00_setup_colab.html#sphx-glr-auto-examples-shortclips-00-setup-colab-py"><span class="std std-ref">Setup Google Colab</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/00_setup_colab.py</span></code>)</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/shortclips/07_extract_motion_energy.html#sphx-glr-auto-examples-shortclips-07-extract-motion-energy-py"><span class="std std-ref">Extract motion energy features from the stimuli</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/07_extract_motion_energy.py</span></code>)</p></td>
 <td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/shortclips/07_extract_motion_energy.html#sphx-glr-auto-examples-shortclips-07-extract-motion-energy-py"><span class="std std-ref">Extract motion energy features from the stimuli</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/shortclips/07_extract_motion_energy.py</span></code>)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/vim2/00_download_vim2.html#sphx-glr-auto-examples-vim2-00-download-vim2-py"><span class="std std-ref">Download the data set from CRCNS</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/vim2/00_download_vim2.py</span></code>)</p></td>
 <td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/vim2/00_download_vim2.html#sphx-glr-auto-examples-vim2-00-download-vim2-py"><span class="std std-ref">Download the data set from CRCNS</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/vim2/00_download_vim2.py</span></code>)</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="_auto_examples/vim2/01_extract_motion_energy.html#sphx-glr-auto-examples-vim2-01-extract-motion-energy-py"><span class="std std-ref">Extract motion energy features from the stimuli</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/vim2/01_extract_motion_energy.py</span></code>)</p></td>
 <td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/vim2/01_extract_motion_energy.html#sphx-glr-auto-examples-vim2-01-extract-motion-energy-py"><span class="std std-ref">Extract motion energy features from the stimuli</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/vim2/01_extract_motion_energy.py</span></code>)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="_auto_examples/vim2/02_plot_ridge_model.html#sphx-glr-auto-examples-vim2-02-plot-ridge-model-py"><span class="std std-ref">Fit a ridge model with motion energy features</span></a> (<code class="docutils literal notranslate"><span class="pre">../tutorials/vim2/02_plot_ridge_model.py</span></code>)</p></td>
 <td><p>00:00.000</p></td>
 <td><p>0.0</p></td>
 </tr>