:orphan:



.. _sphx_glr_auto_examples:

.. _general_examples:

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

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


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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_datasets:

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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 .. figure:: /auto_examples/datasets/images/thumb/sphx_glr_plot_dataset_arithmetic_thumb.png
     :alt: Dataset Arithmetic

     :ref:`sphx_glr_auto_examples_datasets_plot_dataset_arithmetic.py`

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    </div>


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   :hidden:

   /auto_examples/datasets/plot_dataset_arithmetic

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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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 .. figure:: /auto_examples/datasets/images/thumb/sphx_glr_plot_volume_to_vertex_thumb.png
     :alt: Map from Volume to Vertex Data

     :ref:`sphx_glr_auto_examples_datasets_plot_volume_to_vertex.py`

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    </div>


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   :hidden:

   /auto_examples/datasets/plot_volume_to_vertex

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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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 .. figure:: /auto_examples/datasets/images/thumb/sphx_glr_plot_volume_thumb.png
     :alt: Plot Volume Data

     :ref:`sphx_glr_auto_examples_datasets_plot_volume.py`

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    </div>


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   :hidden:

   /auto_examples/datasets/plot_volume

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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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 .. figure:: /auto_examples/datasets/images/thumb/sphx_glr_plot_vertex_thumb.png
     :alt: Plot Vertex Data

     :ref:`sphx_glr_auto_examples_datasets_plot_vertex.py`

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    </div>


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   :hidden:

   /auto_examples/datasets/plot_vertex

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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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 .. figure:: /auto_examples/datasets/images/thumb/sphx_glr_plot_vertex2D_thumb.png
     :alt: Plot 2D Vertex Data

     :ref:`sphx_glr_auto_examples_datasets_plot_vertex2D.py`

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    </div>


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   /auto_examples/datasets/plot_vertex2D

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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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 .. figure:: /auto_examples/datasets/images/thumb/sphx_glr_plot_volume2D_thumb.png
     :alt: Plot 2D Volume Data

     :ref:`sphx_glr_auto_examples_datasets_plot_volume2D.py`

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    </div>


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   :hidden:

   /auto_examples/datasets/plot_volume2D

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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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 .. figure:: /auto_examples/datasets/images/thumb/sphx_glr_plot_vertexRGB_thumb.png
     :alt: Plot RGB Vertex Data

     :ref:`sphx_glr_auto_examples_datasets_plot_vertexRGB.py`

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    </div>


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   :hidden:

   /auto_examples/datasets/plot_vertexRGB

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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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 .. figure:: /auto_examples/datasets/images/thumb/sphx_glr_plot_volumeRGB_thumb.png
     :alt: Plot RGB Volume Data

     :ref:`sphx_glr_auto_examples_datasets_plot_volumeRGB.py`

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    </div>


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   :hidden:

   /auto_examples/datasets/plot_volumeRGB
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_import_surface:

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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 .. figure:: /auto_examples/import_surface/images/thumb/sphx_glr_import_fmriprep_thumb.png
     :alt: Import fmriprep output

     :ref:`sphx_glr_auto_examples_import_surface_import_fmriprep.py`

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    </div>


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   :hidden:

   /auto_examples/import_surface/import_fmriprep
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_quickflat:

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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_sulci_thumb.png
     :alt: Plot sulci on the flatmap

     :ref:`sphx_glr_auto_examples_quickflat_plot_sulci.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_sulci

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_dropout_thumb.png
     :alt: Plot dropout regions on the flatmap

     :ref:`sphx_glr_auto_examples_quickflat_plot_dropout.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_dropout

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_svg_thumb.png
     :alt: Save a 2D static flatmap as SVG

     :ref:`sphx_glr_auto_examples_quickflat_plot_make_svg.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_make_svg

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_png_thumb.png
     :alt: Save a 2D static flatmap as PNG

     :ref:`sphx_glr_auto_examples_quickflat_plot_make_png.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_make_png

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_cutouts_thumb.png
     :alt: Plot cutouts on the flatmap

     :ref:`sphx_glr_auto_examples_quickflat_plot_cutouts.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_cutouts

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_rois_thumb.png
     :alt: Plot ROIs on the flatmap

     :ref:`sphx_glr_auto_examples_quickflat_plot_rois.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_rois

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_connected_vertices_thumb.png
     :alt: Plot which vertices are inside the same voxels

     :ref:`sphx_glr_auto_examples_quickflat_plot_connected_vertices.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_connected_vertices

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_gif_thumb.png
     :alt: Animate a series of volumes as a GIF

     :ref:`sphx_glr_auto_examples_quickflat_plot_make_gif.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_make_gif

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_thickness_nanmean_thumb.png
     :alt: Ignore NaN (not-a-number) values in thickness mapping

     :ref:`sphx_glr_auto_examples_quickflat_plot_thickness_nanmean.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/quickflat/plot_thickness_nanmean

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_zoom_to_roi_thumb.png
     :alt: Plotting a zoomed view of one ROI

     :ref:`sphx_glr_auto_examples_quickflat_plot_zoom_to_roi.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/quickflat/plot_zoom_to_roi

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

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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_figure_thumb.png
     :alt: Plot a 2D static flatmap

     :ref:`sphx_glr_auto_examples_quickflat_plot_make_figure.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_make_figure

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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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 .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_advanced_compositing_thumb.png
     :alt: Plot with advanced compositing

     :ref:`sphx_glr_auto_examples_quickflat_plot_advanced_compositing.py`

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    </div>


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   :hidden:

   /auto_examples/quickflat/plot_advanced_compositing
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_quickstart:

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

Examples demonstrating how to get started with pycortex.




.. raw:: html

    <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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 .. figure:: /auto_examples/quickstart/images/thumb/sphx_glr_retinotopy_webgl_thumb.png
     :alt: Plot Example Retinotopy in Web Viewer

     :ref:`sphx_glr_auto_examples_quickstart_retinotopy_webgl.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/quickstart/retinotopy_webgl

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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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 .. figure:: /auto_examples/quickstart/images/thumb/sphx_glr_show_config_thumb.png
     :alt: Finding out where the config and filestore are

     :ref:`sphx_glr_auto_examples_quickstart_show_config.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/quickstart/show_config

.. raw:: html

    <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...">

.. only:: html

 .. figure:: /auto_examples/quickstart/images/thumb/sphx_glr_plot_retinotopy_flatmap_thumb.png
     :alt: Plot Example Retinotopy Flatmaps

     :ref:`sphx_glr_auto_examples_quickstart_plot_retinotopy_flatmap.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/quickstart/plot_retinotopy_flatmap
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_surface_analyses:

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

Examples demonstrating operations and analyses done on brain surfaces.




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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...">

.. only:: html

 .. figure:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_tissots_indicatrix_thumb.png
     :alt: Tissot's Indicatrix

     :ref:`sphx_glr_auto_examples_surface_analyses_plot_tissots_indicatrix.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/surface_analyses/plot_tissots_indicatrix

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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...">

.. only:: html

 .. figure:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_geodesic_path_thumb.png
     :alt: Plotting Geodesic Paths

     :ref:`sphx_glr_auto_examples_surface_analyses_plot_geodesic_path.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/surface_analyses/plot_geodesic_path

.. raw:: html

    <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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 .. figure:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_geodesic_distance_thumb.png
     :alt: Plotting Geodesic Distances

     :ref:`sphx_glr_auto_examples_surface_analyses_plot_geodesic_distance.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/surface_analyses/plot_geodesic_distance

.. raw:: html

    <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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 .. figure:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_flatmap_distortion_thumb.png
     :alt: Flatmap Distortion

     :ref:`sphx_glr_auto_examples_surface_analyses_plot_flatmap_distortion.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/surface_analyses/plot_flatmap_distortion

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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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 .. figure:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_subsurfaces_thumb.png
     :alt: Plot and Use Subsurface Tools

     :ref:`sphx_glr_auto_examples_surface_analyses_plot_subsurfaces.py`

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    </div>


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   :hidden:

   /auto_examples/surface_analyses/plot_subsurfaces

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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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 .. figure:: /auto_examples/surface_analyses/images/thumb/sphx_glr_plot_interpolate_data_thumb.png
     :alt: Interpolate Data

     :ref:`sphx_glr_auto_examples_surface_analyses_plot_interpolate_data.py`

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    </div>


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   :hidden:

   /auto_examples/surface_analyses/plot_interpolate_data
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_utils:

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

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




.. raw:: html

    <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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 .. figure:: /auto_examples/utils/images/thumb/sphx_glr_plot_get_roi_vertices_thumb.png
     :alt: Get Vertices for an ROI

     :ref:`sphx_glr_auto_examples_utils_plot_get_roi_vertices.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/plot_get_roi_vertices

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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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 .. figure:: /auto_examples/utils/images/thumb/sphx_glr_plot_voxel_distance_from_surface_thumb.png
     :alt: Voxel distance from surface

     :ref:`sphx_glr_auto_examples_utils_plot_voxel_distance_from_surface.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/plot_voxel_distance_from_surface

.. raw:: html

    <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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 .. figure:: /auto_examples/utils/images/thumb/sphx_glr_plot_mosaic_thumb.png
     :alt: Mosaic plot

     :ref:`sphx_glr_auto_examples_utils_plot_mosaic.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/plot_mosaic

.. raw:: html

    <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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 .. figure:: /auto_examples/utils/images/thumb/sphx_glr_subject_to_mni_thumb.png
     :alt: Transform from Subject to MNI Space

     :ref:`sphx_glr_auto_examples_utils_subject_to_mni.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/subject_to_mni

.. raw:: html

    <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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 .. figure:: /auto_examples/utils/images/thumb/sphx_glr_plot_roi_voxel_mask_thumb.png
     :alt: Get ROI Voxel Mask

     :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_mask.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/plot_roi_voxel_mask

.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/utils/images/thumb/sphx_glr_mni_to_subject_thumb.png
     :alt: Transform from MNI to Subject Space

     :ref:`sphx_glr_auto_examples_utils_mni_to_subject.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/mni_to_subject

.. raw:: html

    <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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 .. figure:: /auto_examples/utils/images/thumb/sphx_glr_multi_panels_plots_thumb.png
     :alt: Multi-panels figures

     :ref:`sphx_glr_auto_examples_utils_multi_panels_plots.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/multi_panels_plots

.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/utils/images/thumb/sphx_glr_plot_roi_voxel_index_volume_thumb.png
     :alt: Get ROI Index Volume

     :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_index_volume.py`

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    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/plot_roi_voxel_index_volume
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    <div class="sphx-glr-clear"></div>



.. _sphx_glr_auto_examples_webgl:

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

Examples demonstrating how to make beautiful interactive 3-D viewers




.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/webgl/images/thumb/sphx_glr_single_dataset_thumb.png
     :alt: Create a 3D WebGL Viewer

     :ref:`sphx_glr_auto_examples_webgl_single_dataset.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/webgl/single_dataset

.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/webgl/images/thumb/sphx_glr_static_thumb.png
     :alt: Create a static viewer

     :ref:`sphx_glr_auto_examples_webgl_static.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/webgl/static

.. 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

 .. figure:: /auto_examples/webgl/images/thumb/sphx_glr_dynamic_with_custom_template_thumb.png
     :alt: Dynamic viewer with html template

     :ref:`sphx_glr_auto_examples_webgl_dynamic_with_custom_template.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/webgl/dynamic_with_custom_template

.. 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

 .. figure:: /auto_examples/webgl/images/thumb/sphx_glr_static_with_custom_template_thumb.png
     :alt: Static viewer with html template

     :ref:`sphx_glr_auto_examples_webgl_static_with_custom_template.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/webgl/static_with_custom_template

.. raw:: html

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

.. only:: html

 .. figure:: /auto_examples/webgl/images/thumb/sphx_glr_multiple_datasets_thumb.png
     :alt: Create a 3D WebGL Viewer with Multiple Datasets

     :ref:`sphx_glr_auto_examples_webgl_multiple_datasets.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/webgl/multiple_datasets
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. only :: html

 .. container:: sphx-glr-footer
    :class: sphx-glr-footer-gallery


  .. 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>`


.. only:: html

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    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_