..  BrainVISA website


:doc:`Neuroimaging tools available to the community <applications>`
===================================================================


.. |morphologist| raw:: html

    <div class="imgbox imgbox-main">
      <a href="morphologist.html">
        <img src="_static/images/sulci_map.jpg" style="height: 200px;" />
      </a>
    </div>

.. |cortical_surface| raw:: html

    <div class="imgbox imgbox-main">
      <a href="cortical_surface.html">
        <img src="_static/images/hiphop138_L_left.jpg" style="height: 200px;" />
      </a>
    </div>

.. |anatomist| raw:: html

    <div class="imgbox imgbox-main">
      <a href="anatomist.html">
        <img src="_static/images/fusion_cutmesh_2.png" style="height: 200px;" />
      </a>
    </div>

.. |brainrat| raw:: html

    <div class="imgbox imgbox-main">
      <a href="brainrat.html">
        <img src="_static/images/brainrat_autorad.jpg" style="height: 200px;" />
      </a>
    </div>

.. .. |ric| raw:: html
..
..     <div class="imgbox imgbox-main">
..       <a href="applications.html#ric">
..         <img src="http://www.mdbrain.org/personalpages/peter/front_image.jpg" style="height: 200px;" />
..       </a>
..     </div>
..
.. .. |vobi_one| raw:: html
..
..     <div class="imgbox imgbox-main">
..       <a href="applications.html#vobi_one">
..         <img src="_static/images/vobi_one.png" style="height: 200px;" />
..       </a>
..     </div>

.. |intranat| raw:: html

    <div class="imgbox imgbox-main">
      <a href="applications.html#intranat">
        <img src="https://f-tract.eu/wp-content/uploads/2016/05/logoIntrAnat.png" style="height: 200px;" />
      </a>
    </div>

.. |snapbase| raw:: html

    <div class="imgbox imgbox-main">
      <a href="tools.html#snapbase">
        <img src="images/snapbase.jpg" style="height: 200px;" />
      </a>
    </div>

.. |datamind| raw:: html

    <div class="imgbox imgbox-main">
      <a href="tools.html#datamind">
        <img src="images/datamind.png" style="height: 200px;" />
      </a>
    </div>

.. |highres| raw:: html

    <div class="imgbox imgbox-main">
      <a href="tools.html#highres-cortex-lamintion-of-the-cortex">
        <img src="images/highres-1.jpg" style="width: 148px;" />
        <img src="images/highres-2.jpg" style="width: 148px;" />
      </a>
    </div>

.. |primate| raw:: html

    <div class="imgbox imgbox-main">
      <a href="tools.html#primate">
        <img src="images/primate.png" style="width: 300px;" />
      </a>
    </div>

.. rst-class:: centered-cols

+------------------------------------------------------------------------------+------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| |morphologist|                                                               | |cortical_surface|                                                           | |anatomist|                                                                 |
|                                                                              |                                                                              |                                                                             |
| :doc:`Morphologist: Brain segmentation and sulcal analysis <morphologist>`   | :doc:`Cortical surface analysis <cortical_surface>`                          | :doc:`anatomist`                                                            |
+------------------------------------------------------------------------------+------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| |brainrat|                                                                   | |intranat|                                                                   | |primate|                                                                   |
|                                                                              |                                                                              |                                                                             |
| :doc:`3D histology <brainrat>`                                               | :doc:`Intracranial electrodes implantation <applications>`                   | :ref:`primate`                                                              |
+------------------------------------------------------------------------------+------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| |snapbase|                                                                   | |datamind|                                                                   |                                                                             |
|                                                                              |                                                                              |                                                                             |
| :ref:`snapbase`                                                              | :ref:`datamind`                                                              |                                                                             |
+------------------------------------------------------------------------------+------------------------------------------------------------------------------+-----------------------------------------------------------------------------+


:doc:`Non-released applications <demos_wip>`
============================================

.. |constellation| raw:: html

    <div class="imgbox imgbox-main">
      <a href="demos_wip.html#constellation">
        <img src="_static/images/constellation/all_small_brains.jpg" style="height: 200px;" />
      </a>
    </div>

.. |disco| raw:: html

    <div class="imgbox imgbox-main">
      <a href="demos_wip.html#disco-constraints-based-diffeomorphic-registration">
        <img src="_static/images/disco.png" style="height: 200px;" />
      </a>
    </div>

.. |capsul| image:: _static/images/capsul.jpg
    :height: 200
    :target: ../capsul/index.html

.. |nuclearimaging| raw:: html

    <div class="imgbox imgbox-main">
      <a href="demos_wip.html#nuclear-imaging">
        <img src="_static/images/pet_interface.png" style="height: 200px;" />
      </a>
    </div>

.. |baby| raw:: html

    <div class="imgbox imgbox-main">
      <a href="demos_wip.html#baby">
        <img src="images/baby.jpg" style="height: 200px;" />
      </a>
    </div>

.. |connectomist| raw:: html

    <div class="imgbox imgbox-main">
      <a href="demos_wip.html#connectomist">
        <img src="images/fibers_clustering.jpg" style="height: 200px;" />
      </a>
    </div>

.. |sacha| raw:: html

    <div class="imgbox imgbox-main">
      <a href="demos_wip.html#sacha">
        <img src="images/logo_SACHA_white.jpg" style="width: 300px;" />
      </a>
    </div>

.. |whasa| raw:: html

    <div class="imgbox imgbox-main">
      <a href="demos_wip.html#whasa">
        <img src="images/whasa.jpg" style="height: 150px; position: relative; bottom: 0px; margin-top: 50px;" />
      </a>
    </div>

.. rst-class:: centered-cols

+------------------------------------------------------------------------------+------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| |constellation|                                                              | |disco|                                                                      | |baby|                                                                      |
|                                                                              |                                                                              |                                                                             |
| :ref:`constellation`                                                         | :ref:`disco`                                                                 | :ref:`baby`                                                                 |
+------------------------------------------------------------------------------+------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| |nuclearimaging|                                                             | |highres|                                                                    | |whasa|                                                                     |
|                                                                              |                                                                              |                                                                             |
| :ref:`nuclear_imaging`                                                       | :ref:`highres_cortex`                                                        | :ref:`whasa`                                                                |
+------------------------------------------------------------------------------+------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| |connectomist|                                                               | |sacha|                                                                      |                                                                             |
|                                                                              |                                                                              |                                                                             |
| :ref:`connectomist`                                                          | :ref:`sacha`                                                                 |                                                                             |
+------------------------------------------------------------------------------+------------------------------------------------------------------------------+-----------------------------------------------------------------------------+


:doc:`BrainVISA for you <infrastructure>`
=========================================

.. |axon| image:: _static/images/axon_schema.jpg
    :height: 200
    :target: infrastructure.html#whatsinbv

.. |dev| image:: images/cort_toolbox.png
    :height: 200
    :target: infrastructure.html#integrate

.. rst-class:: centered-cols

+------------------------------------------------------------------------------+------------------------------------------------------------------------------+
| |axon|                                                                       | |dev|                                                                        |
|                                                                              |                                                                              |
| :ref:`whatsinbv`                                                             | :ref:`integrate`                                                             |
+------------------------------------------------------------------------------+------------------------------------------------------------------------------+

Main partners
=============

.. raw:: html

  <table class="centered-cols docutils" style="width: 100%;">
    <colgroup>
    <col width="25%" />
    <col width="25%" />
    <col width="25%" />
    <col width="25%" />
    </colgroup>
    <tbody valign="top">
    <tr class="row-odd">
      <td>
        <div style="display: inline; vertical-align: middle;">
          <a href="http://i2bm.cea.fr">
            <img src="images/labs/cea.jpg" style="height: 70px;" /> &nbsp;
          </a>
          <div style="display: inline-block; vertical-align: middle;">
            <a href="http://i2bm.cea.fr/dsv/i2bm/Pages/NeuroSpin.aspx">
              <img src="images/labs/neurospin.png" style="height: 30px;" />
            </a><br/>
            <a href="http://i2bm.cea.fr/dsv/i2bm/Pages/MIRCen.aspx">
              <img src="images/labs/mircen.png" style="height: 30px;" />
            </a><br/>
            <a href="http://i2bm.cea.fr/dsv/i2bm/Pages/SHFJ.aspx">
              <img src="images/labs/shfj.png" style="height: 30px;" />
            </a>
          </div>
        </div>
        <p>The 3 labs of <a href="http://i2bm.cea.fr">CEA I2BM</a> are developing and maintaining most of the BrainVISA infrastructure.
        </p>
      </td>
      <td>
        <a href="http://cati-neuroimaging.com">
          <img src="images/labs/cati_logo.png" style="width: 250px;" />
        </a>
        <p>
          The <a href="http://cati-neuroimaging.com">CATI Neuroimaging</a> project for neurodegenerative diseases analysis platform has based part of its pipelines and toolboxes on the BrainVISA infrastructure
        </p>
      </td>
      <td>
        <div style="align: block; position: relative; width: 300px; height: 150px;">
          <img src="images/labs/ifr49.png" style="height: 120px; position: absolute; left: 100px; top: 30px; z-index: 1;" />
          <img src="images/labs/inserm.png" style="height: 50px; position: absolute; left: 50px; z-index: 2;" />
        </div>
        <p>The former IFR49 supported by the <a href="http://inserm.fr">Inserm institute</a> has had a large contribution to BrainVISA
        </p>
      </td>
      <td>
        <div><a href="http://www.cnrs.fr/">
          <img src="images/labs/cnrs.png" style=""/></a>
        </div>
        <p>The <a href="http://www.cnrs.fr">CNRS</a> institute has been contributing through several labs, mainly the <a href="http://www.meca-brain.org/">MeCA group</a> and <a href="http://www.aramislab.fr/">ARAMIS lab</a>
        </p>
      </td>
    </tr>
    <tr>
      <td>
        <div><a href="http://www.upmc.fr/">
          <img src="images/labs/upmc_logo.gif" style=""/></a>
        </div>
        <p>The <a href="http://www.upmc.fr">UPMC</a> university has been contributing through several labs
        </p>
      </td>
      <td>
        <div><a href="http://icm-institute.org">
          <img src="images/labs/icm_logo.png" style="height: 120px;"/></a>
        </div>
        <p><a href="http://icm-institute.org">ICM Institut du Cerveau et de la moëlle épinière</a>
        </p>
      </td>
      <td>
        <div><a href="https://www.humanbrainproject.eu/">
          <img src="images/labs/hbp_logo.png" style="height: 120px;" /></a>
        </div>
        <p>The <a href="https://www.humanbrainproject.eu/">Human Brain Project</a> participates to some of the projects.
        </p>
      </td>
    </tr>
    </tbody>
  </table>


Quick links
===========

.. image:: images/cort_contact.png
    :height: 100
    :align: left

.. toctree::
    :maxdepth: 1
    :hidden:

    news
    download
    documentation
    applications
    anatomist
    morphologist
    cortical_surface
    brainrat
    infrastructure
    tools
    changelog
    demos_wip
    publications

.. |cite| raw:: html

    <a href="publications.html#cite-brainvisa">
      <div class="citebutton">
        Cite us
      </div>
    </a>

.. hlist::
    :columns: 3

    * :doc:`news`
    * :doc:`download`
    * :doc:`documentation`
    * :doc:`applications`
    * :doc:`anatomist`
    * :doc:`morphologist`
    * :doc:`cortical_surface`
    * :doc:`brainrat`
    * :doc:`infrastructure`
    * :doc:`tools`
    * :ref:`integrate`
    * :doc:`changelog`
    * :doc:`demos_wip`
    * :doc:`publications`
    * :doc:`support`
    * |cite|


Search
=======

.. image:: images/cort.png
    :height: 100
    :align: left
    :target: search.html

.. |french| image:: images/francais.png
  :height: 20
  :target: french.html

* :ref:`search`
* :doc:`gsearch`
* :doc:`legal`
* |french| :doc:`French site <french>`

.. toctree::
  :hidden:

  gsearch
  legal
  french
  download-4.6
  support
  configuration
  brainvisa_research_license

:Release: |release|
:Date: |today|