:orphan:

.. _general_examples:

Example Gallery
================

.. contents:: Contents
   :local:
   :depth: 2



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Datasets Examples
------------------------------

Examples demonstrating how to create, manipulate, plot datasets.




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    <div class="sphx-glr-thumbcontainer" tooltip="This plots example volume data onto an example subject, S1, onto a flatmap using quickflat. In ...">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_dataset_arithmetic_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_dataset_arithmetic.py`

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      <div class="sphx-glr-thumbnail-title">Dataset Arithmetic</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In order to move from Volume data to Vertex data, you start with data from voxels and then crea...">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_volume_to_vertex_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_volume_to_vertex.py`

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      <div class="sphx-glr-thumbnail-title">Map from Volume to Vertex Data</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This plots example volume data onto an example subject, S1, onto a flatmap using quickflat. In ...">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_volume_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_volume.py`

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      <div class="sphx-glr-thumbnail-title">Plot Volume Data</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This plots example vertex data onto an example subject, S1, onto a flatmap using quickflat. In ...">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_vertex_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_vertex.py`

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      <div class="sphx-glr-thumbnail-title">Plot Vertex Data</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This plots example 2D vertex data onto an example subject, S1, onto a flatmap using quickflat. ...">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_vertex2D_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_vertex2D.py`

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      <div class="sphx-glr-thumbnail-title">Plot 2D Vertex Data</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This plots example volume data onto an example subject, S1, onto a flatmap using quickflat. In ...">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_volume2D_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_volume2D.py`

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      <div class="sphx-glr-thumbnail-title">Plot 2D Volume Data</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This plots example RGB vertex data onto an example subject, S1, onto a flatmap using quickflat....">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_vertexRGB_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_vertexRGB.py`

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      <div class="sphx-glr-thumbnail-title">Plot RGB Vertex Data</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This plots an example RGB dataset onto an example subject, S1, onto a flatmap using quickflat. ...">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_volumeRGB_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_volumeRGB.py`

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      <div class="sphx-glr-thumbnail-title">Plot RGB Volume Data</div>
    </div>


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    </div>

Examples with fsaverage
------------------------------

Examples showing how to use PyCortex to visualize data on fsaverage.


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how data in a lower resolution fsaverage template  (e.g., fsaverage5 or fsav...">

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  .. image:: /auto_examples/fsaverage/images/thumb/sphx_glr_upsample_to_fsaverage_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_fsaverage_upsample_to_fsaverage.py`

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      <div class="sphx-glr-thumbnail-title">Upsample data from a lower resolution fsaverage template to fsaverage for visualization</div>
    </div>


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    </div>

Importing Surfaces Examples
------------------------------

Examples demonstrating how to import surfraces from other software (e.g.
FreeSurfer, fmriprep).




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    <div class="sphx-glr-thumbcontainer" tooltip="Recently, many people have start to use fmriprep as a complete preprocessing workflow of anatom...">

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  .. image:: /auto_examples/import_surface/images/thumb/sphx_glr_import_fmriprep_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_import_surface_import_fmriprep.py`

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      <div class="sphx-glr-thumbnail-title">Import fmriprep output</div>
    </div>


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    </div>

Quickflat Examples
------------------------------

Examples demonstrating how to create flatmaps.




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    <div class="sphx-glr-thumbcontainer" tooltip="The sulci are defined in a sub-layer of the sulci layer in &lt;filestore&gt;/&lt;subject&gt;/overlays.svg.">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_sulci_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_sulci.py`

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      <div class="sphx-glr-thumbnail-title">Plot sulci on the flatmap</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="A dropout region is a region with very low EPI signal. In pycortex a crosshatch is used to disp...">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_dropout_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_dropout.py`

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      <div class="sphx-glr-thumbnail-title">Plot dropout regions on the flatmap</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Plot a 2D static flatmap and save it as PNG file.">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_png_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_make_png.py`

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      <div class="sphx-glr-thumbnail-title">Save a 2D static flatmap as PNG</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Plot a 2D static flatmap and save it as SVG file.">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_svg_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_make_svg.py`

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      <div class="sphx-glr-thumbnail-title">Save a 2D static flatmap as SVG</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Cutouts are manually generated cuts of the cortical surface to highlight a region of interest.">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_cutouts_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_cutouts.py`

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      <div class="sphx-glr-thumbnail-title">Plot cutouts on the flatmap</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="ROIs are defined as sub-layers of the roi layer in &lt;filestore&gt;/&lt;subject&gt;/overlays.svg">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_rois_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_rois.py`

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      <div class="sphx-glr-thumbnail-title">Plot ROIs on the flatmap</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Show lines connecting vertices on the flatmap that are actually within the same voxels in a giv...">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_connected_vertices_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_connected_vertices.py`

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      <div class="sphx-glr-thumbnail-title">Plot which vertices are inside the same voxels</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="A convenient way to compare two flat maps (e.g., prediction performance or tuning weights) is t...">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_gif_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_make_gif.py`

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      <div class="sphx-glr-thumbnail-title">Animate a series of volumes as a GIF</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="By default, pycortex quickshow averages across the thickness of the cortex for each pixel in th...">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_thickness_nanmean_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_thickness_nanmean.py`

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      <div class="sphx-glr-thumbnail-title">Ignore NaN (not-a-number) values in thickness mapping</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Sometimes it is useful to create a flatmap that is zoomed in one just a single ROI. The locatio...">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_zoom_to_roi_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_zoom_to_roi.py`

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      <div class="sphx-glr-thumbnail-title">Plotting a zoomed view of one ROI</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="quickflat visualizations use matplotlib to generate figure-quality 2D flatmaps.">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_figure_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_make_figure.py`

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      <div class="sphx-glr-thumbnail-title">Plot a 2D static flatmap</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The way flatmap plotting works in pycortex is to create different image layers (data, ROIs, sul...">

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  .. image:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_advanced_compositing_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickflat_plot_advanced_compositing.py`

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      <div class="sphx-glr-thumbnail-title">Plot with advanced compositing</div>
    </div>


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    </div>

Quickstart Examples
------------------------------

Examples demonstrating how to get started with pycortex.




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    <div class="sphx-glr-thumbcontainer" tooltip="This demo shows how to plot example retinotopy data onto a subject&#x27;s brain in a web viewer. In ...">

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  .. image:: /auto_examples/quickstart/images/thumb/sphx_glr_retinotopy_webgl_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickstart_retinotopy_webgl.py`

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      <div class="sphx-glr-thumbnail-title">Plot Example Retinotopy in Web Viewer</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Easily locating your config file and filestore locations. This comes in useful when things don&#x27;...">

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  .. image:: /auto_examples/quickstart/images/thumb/sphx_glr_show_config_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickstart_show_config.py`

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      <div class="sphx-glr-thumbnail-title">Finding out where the config and filestore are</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This demo shows how to plot example retinotopy data onto a subject&#x27;s brain on a flatmap. In ord...">

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  .. image:: /auto_examples/quickstart/images/thumb/sphx_glr_plot_retinotopy_flatmap_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_quickstart_plot_retinotopy_flatmap.py`

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      <div class="sphx-glr-thumbnail-title">Plot Example Retinotopy Flatmaps</div>
    </div>


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    </div>

Surface Analysis Examples
------------------------------

Examples demonstrating operations and analyses done on brain surfaces.




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    <div class="sphx-glr-thumbnails">


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    <div class="sphx-glr-thumbcontainer" tooltip="Creating a flatmap from a folded cortical surface always introduces some distortion. This is si...">

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  .. image:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_tissots_indicatrix_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_surface_analyses_plot_tissots_indicatrix.py`

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      <div class="sphx-glr-thumbnail-title">Tissot's Indicatrix</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This will plot a geodesic path between two vertices on the cortical surface. This path is based...">

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  .. image:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_geodesic_path_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_surface_analyses_plot_geodesic_path.py`

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      <div class="sphx-glr-thumbnail-title">Plotting Geodesic Paths</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This plots the distances (in mm) between a vertex or set of vertices and all other vertices on ...">

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  .. image:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_geodesic_distance_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_surface_analyses_plot_geodesic_distance.py`

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      <div class="sphx-glr-thumbnail-title">Plotting Geodesic Distances</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Creating a flatmap from a folded cortical surface always introduces some distortion. This is si...">

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  .. image:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_flatmap_distortion_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_surface_analyses_plot_flatmap_distortion.py`

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      <div class="sphx-glr-thumbnail-title">Flatmap Distortion</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Subsurfaces can be used for efficient operations on subsets of cortical surface">

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  .. image:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_subsurfaces_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_surface_analyses_plot_subsurfaces.py`

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      <div class="sphx-glr-thumbnail-title">Plot and Use Subsurface Tools</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example we show how to interpolate data from a sparse collection of points to all the p...">

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  .. image:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_interpolate_data_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_surface_analyses_plot_interpolate_data.py`

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      <div class="sphx-glr-thumbnail-title">Interpolate Data</div>
    </div>


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    </div>

Utility Examples
------------------------------

Examples demonstrating how to do all sorts of beautiful things using pycortex. 




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    <div class="sphx-glr-thumbcontainer" tooltip="In this example we show how to get the vertices that are inside an ROI that was defined in the ...">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_get_roi_vertices_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_utils_plot_get_roi_vertices.py`

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      <div class="sphx-glr-thumbnail-title">Get Vertices for an ROI</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The utility function get_vox_dist returns the distance from each voxel in some space to the nea...">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_voxel_distance_from_surface_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_utils_plot_voxel_distance_from_surface.py`

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      <div class="sphx-glr-thumbnail-title">Voxel distance from surface</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The function mosaic plots all of the slices in a volume in a matplotlib figure. Good for quick ...">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_mosaic_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_utils_plot_mosaic.py`

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      <div class="sphx-glr-thumbnail-title">Mosaic plot</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Pycortex has built-in functionality for linearly transforming data to and from standard atlas s...">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_subject_to_mni_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_utils_subject_to_mni.py`

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      <div class="sphx-glr-thumbnail-title">Transform from Subject to MNI Space</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Get proportion of each voxel that exists within a named ROI (this  constitutes a probability ma...">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_roi_voxel_mask_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_mask.py`

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      <div class="sphx-glr-thumbnail-title">Get ROI Voxel Mask</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Pycortex has built-in functionality for linearly transforming data to and from standard atlas s...">

.. only:: html

  .. image:: /auto_examples/utils/images/thumb/sphx_glr_mni_to_subject_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_utils_mni_to_subject.py`

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      <div class="sphx-glr-thumbnail-title">Transform from MNI to Subject Space</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The function cortex.export.plot_panels plots a number of 3d views of a given volume, in the sam...">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_multi_panels_plots_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_utils_multi_panels_plots.py`

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      <div class="sphx-glr-thumbnail-title">Multi-panels figures</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Create an index volume (similar to the aseg masks in freesurfer) with a different  integer inde...">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_roi_voxel_index_volume_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_index_volume.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Get ROI Index Volume</div>
    </div>


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    </div>

WebGL Examples
------------------------------

Examples demonstrating how to make beautiful interactive 3-D viewers




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    <div class="sphx-glr-thumbnails">


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A webgl viewer displays a 3D view of brain data in a web browser">

.. only:: html

  .. image:: /auto_examples/webgl/images/thumb/sphx_glr_single_dataset_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_webgl_single_dataset.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Create a 3D WebGL Viewer</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A static viewer is a brain viewer that exists permanently on a filesystem">

.. only:: html

  .. image:: /auto_examples/webgl/images/thumb/sphx_glr_static_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_webgl_static.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Create a static viewer</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Pycortex has the functionality of provide a custom html template to specify  the attributes of ...">

.. only:: html

  .. image:: /auto_examples/webgl/images/thumb/sphx_glr_dynamic_with_custom_template_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_webgl_dynamic_with_custom_template.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Dynamic viewer with html template</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Pycortex has the functionality of provide a custom html template to specify  the attributes of ...">

.. only:: html

  .. image:: /auto_examples/webgl/images/thumb/sphx_glr_static_with_custom_template_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_webgl_static_with_custom_template.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Static viewer with html template</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="A webgl viewer displays a 3D view of brain data in a web browser">

.. only:: html

  .. image:: /auto_examples/webgl/images/thumb/sphx_glr_multiple_datasets_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_webgl_multiple_datasets.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Create a 3D WebGL Viewer with Multiple Datasets</div>
    </div>


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    </div>


.. toctree::
   :hidden:
   :includehidden:


   /auto_examples/datasets/index.rst
   /auto_examples/fsaverage/index.rst
   /auto_examples/import_surface/index.rst
   /auto_examples/quickflat/index.rst
   /auto_examples/quickstart/index.rst
   /auto_examples/surface_analyses/index.rst
   /auto_examples/utils/index.rst
   /auto_examples/webgl/index.rst


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    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


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