.. _sphx_glr_auto_examples_utils:

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 SVG ROI file (see /rois.rst).">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_get_roi_vertices_thumb.png
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  :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>
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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 nearest vertex on the given surface. This function is used for generating ROI masks, cortical masks, etc.">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_voxel_distance_from_surface_thumb.png
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  :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>
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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 visualization or testing of volumes.">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_mosaic_thumb.png
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  :ref:`sphx_glr_auto_examples_utils_plot_mosaic.py`

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      <div class="sphx-glr-thumbnail-title">Mosaic plot</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 spaces (e.g. MNI-152). This functionality is built on top of FSL.">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_subject_to_mni_thumb.png
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  :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>
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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 map for the ROI, with values ranging from 0-1). Plot this probabilistic roi mask onto a flatmap. ">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_roi_voxel_mask_thumb.png
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  :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>
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    <div class="sphx-glr-thumbcontainer" tooltip="Pycortex has built-in functionality for linearly transforming data to and from standard atlas spaces (e.g. MNI-152). This functionality is built on top of FSL.">

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  .. 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 same matplotlib figure. It does that by saving a temporary image for each view, and then aggregating them in the same figure.">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_multi_panels_plots_thumb.png
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  :ref:`sphx_glr_auto_examples_utils_multi_panels_plots.py`

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      <div class="sphx-glr-thumbnail-title">Multi-panels figures</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 index for each ROI. ROIs in the left hemisphere will have negative values, ROIs in the right hemisphere will have positive values.">

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  .. image:: /auto_examples/utils/images/thumb/sphx_glr_plot_roi_voxel_index_volume_thumb.png
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  :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_index_volume.py`

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


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    </div>


.. toctree::
   :hidden:

   /auto_examples/utils/plot_get_roi_vertices
   /auto_examples/utils/plot_voxel_distance_from_surface
   /auto_examples/utils/plot_mosaic
   /auto_examples/utils/subject_to_mni
   /auto_examples/utils/plot_roi_voxel_mask
   /auto_examples/utils/mni_to_subject
   /auto_examples/utils/multi_panels_plots
   /auto_examples/utils/plot_roi_voxel_index_volume