Anatomist: Data visualization and library of high-level neuroimaging graphical components

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Tutorial: :anatomist:`Tutorial <user_doc/anatomist_tutorial.html>`

Full documentation: :anatomist:`Handbook <user_doc/anatomist_manual1.html>`

:anatomist:`Slides on the referentials system <anatomist_referentials.pdf>`

:anatomist:`Developers documentation <dev_doc/index.html>`

* In C++: :anadox:`Anatomist library API doc <index.html>`
* In Python: :pyanatomist:`PyAnatomist <index.html>`

anatomist: data visualization and library of high-level neuroimaging graphical components

"Builtin" toolboxes, shipped with the main BrainVISA distribution

“Builtin” toolboxes, shipped with the main BrainVISA distribution

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      <th class="head">Author or Lab</th>
      <th class="head">BV versions</th>
      <th class="head">Systems</th>
      <th class="head">Short desription</th>
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      <a href="morphologist.html">

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    <a href="morphologist.html">Morphologist toolbox</a>
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  <td><a href="https://joliot.cea.fr/drf/joliot/Pages/Entites_de_recherche/neurospin/unati.aspx">UNATI, CEA</a></td>
  <td>all</td>
  <td>T1 MRI segmentation, cortical sulci recognition and morphometry toolbox</td>
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    <a href="cortical_surface.html">

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    <a href="cortical_surface.html">Cortical surface toolbox</a>
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  <td><a href="https://www.lis-lab.fr/">LSIS, CNRS</a></td>
  <td>3.1 or &gt;</td>
  <td>Cortical surface parameterization and analysis
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    </a>
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  <td>
    <a href="brainrat.html">BrainRAT toolbox</a>
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  <td>BioPICSEL, MIRCEN, CEA
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  <td>Ex vivo 3D reconstruction and analysis</td>
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      <img src="https://surfer.nmr.mgh.harvard.edu/fscortex.png" align="center" style="height: 192px;" />
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  <td>Freesurfer toolbox</td>
  <td><a href="http://lnao.fr">LNAO, CEA</a></td>
  <td>4.2 or &gt;</td>
  <td>Link between Morphologist toolbox and <a href="https://surfer.nmr.mgh.harvard.edu/">FreeSurfer software</a>.</td>
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    <a href="anatomist.html">

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    </a>
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  <td><a href="anatomist.html">Anatomist</a></td>
  <td>Interactive 3D visualization</td>
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      <a href="tools.html#snapbase">
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  <td>
    <a href="tools.html#snapbase">SnapBase</a>
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  <td><a href="https://joliot.cea.fr/drf/joliot/Pages/Entites_de_recherche/neurospin/unati.aspx">UNATI</a> / <a href="https://cati-neuroimaging.com">CATI</a></td>
  <td>All
  </td>
  <td>Snapshots and posters renderings for large databases, based on Anatomist, designed to ease quality check.
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  <td>
      <a href="tools.html#datamind">
        <img src="images/datamind.png" style="height: 192px;" />
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  <td>
    <a href="tools.html#datamind">DataMind</a>
  </td>
  <td><a href="https://joliot.cea.fr/drf/joliot/Pages/Entites_de_recherche/neurospin/unati.aspx">Neurospin</a></td>
  <td>All
  </td>
  <td>Statistical analysis and data mining toolbox
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      <a href="tools.html#highres-cortex-lamintion-of-the-cortex">
        <img src="images/highres-1.jpg" style="height: 192px;" />
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    <a href="tools.html#highres-cortex-lamintion-of-the-cortex">HighRes Cortex</a>
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  <td><a href="https://joliot.cea.fr/drf/joliot/Pages/Entites_de_recherche/neurospin/unati.aspx">NeuroSpin</a></td>
  <td>All
  </td>
  <td>Analysis of the laminar structure of the cortex in high resolution MRI
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        </a>
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      <a href="tools.html#primate">Primatologist</a>
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    <td>BioPICSEL, MIRCEN, CEA</td>
    <td>all</td>
    <td>All
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    <td>Segmentation toolbox dedicated to primate brain images
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"builtin" toolboxes, shipped with the main brainvisa distribution

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  <a name="intranat" />
    <td>
      <a href="https://f-tract.eu/software/intranat/"><img src="https://f-tract.eu/wp-content/uploads/2016/05/logoIntrAnat.png" /></a>
    </td>
    <td>
      <a href="https://f-tract.eu/software/intranat/">IntrAnat<a>
    </td>
    <td><a href="https://neurosciences.univ-grenoble-alpes.fr/">Grenoble Institute of Neuroscience</a></td>
    <td>4.3-5.0</td>
    <td>Linux
    </td>
    <td>IntrAnat is a collection of software to manage, analyse and anatomical (MRI, CT) and functional SEEG data (Intracranial electrodes) of epileptic patients.
    </td>
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    <td>
      <div class="imgbox" style="height: 192px; width: auto">
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    </td>
    <td>
      <a href="https://www.nitrc.org/projects/brainvisa_ext">RIC</a>
    </td>
    <td><a href="http://www.mdbrain.org/personalpages/peter/index.html">Peter Kochunov</a></td>
    <td>Linux
    </td>
    <td>Cortical thickness maps, gyrification index, sulcal length and depth, NIFTI and NEMA formats converters...
    </td>
  </tr>
  <a name="vobi_one" />
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        <!-- a href="https://trac.int.univ-amu.fr/vobi_one"--><img src="_static/images/vobi_one.png" align="center" style="height: 192px;" />
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    </td>
    <td><!--a href="https://trac.int.univ-amu.fr/vobi_one" -->Vobi One<!--/a--></td>
    <td><a href="https://www.int.univ-amu.fr/">INT, CNRS</a></td>
    <td>currently tested only with 4.3</td>
    <td>Linux
    </td>
    <td>Data processing for functional optical imaging
    </td>
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A. Dubois, J. Dauguet, N. Souedet, A. S. Hérard, D. Rivière, Y. Cointepas, G. Bonvento, P. Hantraye, and T. Delzescaux: **BrainRAT: Brain Reconstruction and Analysis Toolbox. a freely available toolbox for the 3D reconstruction of anatomo-functional brain sections in rodents**, In *38th annual meeting of the Society for Neuroscience*, Washington, 2008.

Dubois, J. Dauguet, N. Souedet, A. S. Hérard, D. Rivière, Y. Cointepas, G. Bonvento, P. Hantraye, and T. Delzescaux: **BrainRAT: Brain Reconstruction and Analysis Toolbox. a freely available toolbox for the 3D reconstruction of anatomo-functional brain sections in rodents**, In *38th annual meeting of the Society for Neuroscience*, Washington, 2008.

Dubois, J. Dauguet, N. Souedet, A. S. Hérard, D. Rivière, Y. Cointepas, G. Bonvento, P. Hantraye, and T. Delzescaux: 

**BrainRAT: Brain Reconstruction and Analysis Toolbox. a freely available toolbox for the 3D reconstruction of anatomo-functional brain sections in rodents**

BrainRAT: Brain Reconstruction and Analysis Toolbox. a freely available toolbox for the 3D reconstruction of anatomo-functional brain sections in rodents

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    </style></head><body dir="ltr" style="max-width:8.5in;margin-top:0.7874in; margin-bottom:0.7874in; margin-left:0.7874in; margin-right:0.7874in; "><ol><li><p class="P26" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span>BrainVISA Research <span class="T14">L</span>icense: free distribution license agreement exclusively for non-commercial research<span class="odfLiEnd"/> </p></li><li><h class="P21" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Preamble">Preamble</a><span class="odfLiEnd"/> </h></li></ol><p class="Standard"><span class="T1">This agreement is a royalty free software license whose purpose is to grant users the freedom to use, modify and redistribute the software </span><span class="T8">licensed hereunder</span><span class="T1"> for research </span><span class="T8">purpose excluding</span><span class="T1"> any commercial use.</span></p><p class="P8">The exercise of these freedoms is subject to certain obligations on users in order to preserve this status during subsequent redistributions. The accessibility of the source code and the rights to copy, modify and redistribute it have the counterpart of offering users only a limited guarantee and imposing only a limited liability on the author of the software, the holder of the economic rights and the successive licensors.</p><p class="P1"><span class="T1">In consideration of access to the </span><span class="T9">software</span><span class="T1"> and the rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors only have limited liability. </span></p><p class="Text_20_body">In this respect, the risks associated with loading, using, modifying and/or developing or reproducing the software by the user are brought to the user's attention, given its <span class="T16">near open source </span>status, which may make it complicated to use, with the result that its use is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the suitability of the software as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions of security. This Agreement may be freely reproduced and published, provided it is not altered, and that no provisions are either added or removed herefrom.</p><p class="Text_20_body">This Agreement may apply to any or all software for which the holder of the economic rights decides to submit the use thereof to its provisions.</p><ol><li><h class="P22" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_1_-_DEFINITIONS">Article 1 - DEFINITIONS</a><span class="odfLiEnd"/> </h></li></ol><p class="P4">For the purpose of this Agreement, when the following expressions commence with a capital letter, they shall have the following meaning:</p><p class="Text_20_body"><span class="T15">Agreement</span>: means this license agreement, and its possible subsequent versions and annexes. </p><p class="Text_20_body"><span class="T15">Software</span>: means the software in its Object Code and/or Source Code form and, where applicable, its documentation, "as is" when the Licensee accepts the Agreement. </p><p class="Text_20_body"><span class="T15">Initial Software</span>: means the Software in its Source Code and possibly its Object Code form and, where applicable, its documentation, "as is" when it is first distributed under the terms and conditions of the Agreement. </p><p class="Text_20_body"><span class="T15">Modified Software</span>: means the Software modified by at least one Contribution. </p><p class="Text_20_body"><span class="T15">Source Code</span>: means all the Software's instructions and program lines to which access is required so as to modify the Software. </p><p class="Text_20_body"><span class="T15">Object Code</span>: means the binary files originating from the compilation of the Source Code. </p><p class="Text_20_body"><span class="T15">Holder</span>: means the holder(s) of the economic rights over the Initial Software. </p><p class="Text_20_body"><span class="T15">Licensee</span>: means the Software user(s) having accepted the Agreement. </p><p class="Text_20_body"><span class="T15">Contributor</span>: means a Licensee having made at least one Contribution. </p><p class="Text_20_body"><span class="T15">Licensor</span>: means the Holder, or any other individual or legal entity, who distributes the Software under the Agreement. </p><p class="Text_20_body"><span class="T15">Contribution</span>: means any or all modifications, corrections, translations, adaptations and/or new functions integrated into the Software by any or all Contributors, as well as any or all Internal Modules. </p><p class="Text_20_body"><span class="T15">Parties</span>: mean both the Licensee and the Licensor. </p><p class="Text_20_body">These expressions may be used both in singular and plural form.</p><ol><li><h class="P22" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_2_-_PURPOSE">Article 2 - <span class="T17">PURPOSE</span></a><span class="odfLiEnd"/> </h></li></ol><p class="P7"><span class="T1">The object of the Agreement is the grant by the Licensor to the Licensee of a non-exclusive, transferable and worldwide license of the Software as defined below in Article </span><span class="T10">5</span><span class="T1"> for the entire term of protection of the Software's rights for research purposes only.</span></p><ol><li><h class="P22" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_3_-_ACCEPTANCE">Article 3 - ACCEPTANCE</a><span class="odfLiEnd"/> </h></li></ol><p class="P17"><span class="T2">3.1</span><span class="T6"> The Licensee shall be deemed as having accepted the terms and conditions of this Agreement upon the occurrence of the first of the following events:</span></p><p class="P19"><span class="T15">(i)</span> loading the Software by any or all means, notably, by downloading from a remote server, or by loading from a physical medium;</p><p class="P19"><span class="T15">(ii)</span> the first time the Licensee exercises any of the rights granted hereunder. </p><p class="Text_20_body"><span class="T15">3.2</span> One copy of the Agreement, containing a notice relating to the characteristics of the Software, to the limited warranty, and to the fact that its use is restricted to experienced users has been provided to the Licensee prior to its acceptance as set forth in Article <span class="T17">3.1</span> hereinabove, and the Licensee hereby acknowledges that it has read and understood it.</p><ol><li><h class="P23" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_4_-_EFFECTIVE_DATE_AND_TERM">Article 4 - EFFECTIVE DATE AND TERM</a><span class="odfLiEnd"/> </h></li></ol><h3 class="Heading_20_3"><a id="a__4_1_EFFECTIVE_DATE"><span/></a>4.1 EFFECTIVE DATE</h3><p class="Text_20_body">The Agreement shall become effective on the date when it is accepted by the Licensee as set forth in Article <span class="T25">3.1.</span></p><h3 class="Heading_20_3"><a id="a__4_2_TERM"><span/></a><a id="term"/>4.2 TERM</h3><p class="Text_20_body">The Agreement shall remain in force for the entire legal term of protection of the economic rights over the Software.</p><ol><li><h class="P22" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_5_-_SCOPE_OF_CONCEDED_RIGHTS">Article <span class="T17">5</span> - SCOPE OF CONCEDED RIGHTS</a><span class="odfLiEnd"/> </h></li></ol><p class="P7"><span class="T1">Notwithstanding the terms of section </span><span class="T11">5</span><span class="T1">.4, Licensor grants to Licensee the following rights to the Software solely for research purposes and for the duration of the Agreement under the conditions detailed below.</span></p><ol><li><ol><li><h class="P24" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__5_1_right_of_use"><span class="T17">5</span>.1 right of use</a><span class="odfLiEnd"/> </h></li></ol></li></ol><p class="P8">The Licensee is authorized to use the Software only for research purposes, it being specified below that this includes:</p><ol><li><p class="P10" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">1.</span>the permanent or temporary reproduction of the Software in whole or in part by any means and in any form.<span class="odfLiEnd"/> </p></li><li><p class="P10" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">2.</span>loading, displaying, executing, or storing the Software in any medium.<span class="odfLiEnd"/> </p></li><li><p class="P9" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">3.</span><span class="T1">the opportunity to observe, study, or test its operation in order to determine the ideas and principles underlying any element of this Software; and this, when the Licensee performs any operation of loading, displaying, executing, transmitting or storing the Software that it is entitled to perform under the </span><span class="T5">Agreement</span><span class="T1">.</span><span class="odfLiEnd"/> </p></li></ol><ol><li><ol><li><h class="P24" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__5_2_right_to_make_contributions"><span class="T17">5</span>.2 right to make contributions</a><span class="odfLiEnd"/> </h></li></ol></li></ol><p class="P8">The right to make Contributions includes the right to translate, adapt, arrange or make any other modification to the Software and the right to reproduce the resulting software. The Licensee is authorized to make any Contribution to the Software provided that it explicitly mentions its name as the author of such Contribution and the date of its creation.</p><ol><li><ol><li><h class="P24" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__5_3_DISTRIBUTION_RIGHT"><span class="T17">5</span>.3 DISTRIBUTION RIGHT</a><span class="odfLiEnd"/> </h></li></ol></li></ol><p class="P8">The distribution right includes in particular the right to distribute, transmit and communicate the Software to the public on any medium, by any means and for research purposes.</p><p class="P8">The Licensee is authorized to distribute copies of the Software, modified or not, to third parties under the conditions detailed below.</p><ol><li><ol><li><ol><li><h class="P25" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__5_3_1_DISTRIBUTION_OF_THE_SOFTWARE_WITHOUT_MODIFICATION"><span class="T17">5</span>.3.1 DISTRIBUTION OF THE SOFTWARE WITHOUT MODIFICATION</a><span class="odfLiEnd"/> </h></li></ol></li></ol></li></ol><p class="P7"><span class="T1">The Licensee is authorized to distribute certified copies of the Software, in Source Code or Object Code form, provided that such distribution complies with the provisions of the </span><span class="T5">Agreement</span><span class="T1"> in their entirety and is accompanied:</span></p><ol><li><p class="P15" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">1.</span>a copy of the Agreement,<span class="odfLiEnd"/> </p></li><li><p class="P15" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">2.</span><span class="T1">a warning regarding the limitation of the Licensor's warranty and liability as provided for in Articles </span><span class="T11">8</span><span class="T1"> and </span><span class="T11">9</span><span class="T1">,</span><span class="odfLiEnd"/> </p></li><li><p class="P11" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">3.</span>and that, in the event that only the Object Code of the Software is redistributed, the Licensee allows effective access to the complete Software Source Code for a period of at least 3 years from the distribution of the Software, it being understood that the additional cost of acquiring the Source Code shall not exceed the simple cost of transferring the data.<span class="odfLiEnd"/> </p></li></ol><ol><li><ol><li><ol><li><h class="P25" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__5_3_2_DISTRIBUTION_OF_THE_MODIFIED_SOFTWARE"><span class="T17">5</span>.3.2 DISTRIBUTION OF THE MODIFIED SOFTWARE</a><span class="odfLiEnd"/> </h></li></ol></li></ol></li></ol><p class="P7"><span class="T1">When the Licensee makes a Contribution to the Software, the conditions of distribution of the resulting Modified Software are then subject to all the provisions of the </span><span class="T5">Agreement</span><span class="T1">.</span></p><p class="P7"><span class="T1">The Licensee is authorized to distribute the Modified Software, in source code or object code form, provided that such distribution complies with the provisions of the </span><span class="T5">Agreement</span><span class="T1"> in their entirety and is accompanied:</span></p><ol><li><p class="P16" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">1.</span>a copy of the Agreement,<span class="odfLiEnd"/> </p></li><li><p class="P16" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">2.</span><span class="T1">a warning regarding the limitation of the Licensor's warranty and liability as provided for in Articles </span><span class="T11">8</span><span class="T1"> and </span><span class="T11">9</span><span class="T1">,</span><span class="odfLiEnd"/> </p></li><li><p class="P12" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">3.</span>and, in the event that only the object code of the Modified Software is redistributed, a note specifying the conditions for effective access to the complete source code of the Modified Software, for a period of at least 3 years from the distribution of the Modified Software, it being understood that the additional cost of acquiring the source code shall not exceed the simple cost of transferring the data.<span class="odfLiEnd"/> </p></li></ol><ol><li><ol><li><h class="P24" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__5_4_-_EXCLUSION"><span class="T17">5</span>.4 - EXCLUSION</a><span class="odfLiEnd"/> </h></li></ol></li></ol><p class="P8">The rights granted by this license exclude any commercial use of the Software.A use of the Software is said to be commercial when a remuneration is received directly or indirectly. This includes, but is not limited to, the following:</p><ul><li><p class="P13" style="margin-left:0cm;"><span class="ListLabel_20_28" style="display:block;float:left;min-width:NaNcm;"></span>the use or integration of all or part of the Software or the Modified Software in a product (software or not) that will be sold or made usable by third parties for a fee,<span class="odfLiEnd"/> </p></li><li><p class="P13" style="margin-left:0cm;"><span class="ListLabel_20_28" style="display:block;float:left;min-width:NaNcm;"></span>the use of all or part of the Software or the Modified Software in research aimed at developing commercial products (software or not),<span class="odfLiEnd"/> </p></li><li><p class="P13" style="margin-left:0cm;"><span class="ListLabel_20_28" style="display:block;float:left;min-width:NaNcm;"></span>the use of all or part of the Software or the Modified Software to provide a service for a fee.<span class="odfLiEnd"/> </p></li></ul><p class="P8">If you are interested in a commercial use of the Software, you must contact its authors in order to receive authorization under the conditions they will set. </p><ol><li><h class="P22" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_6_-_INTELLECTUAL_PROPERTY">Article <span class="T18">6</span> - INTELLECTUAL PROPERTY</a><span class="odfLiEnd"/> </h><ol><li><h class="P24" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__6_1_ON_THE_INITIAL_SOFTWARE"><span class="T18">6</span>.1 ON THE INITIAL SOFTWARE</a><span class="odfLiEnd"/> </h></li></ol></li></ol><p class="P4">The Holder owns the economic rights over the Initial Software. Any or all use of the Initial Software is subject to compliance with the terms and conditions under which the Holder has elected to distribute its work and no one shall be entitled to modify the terms and conditions for the distribution of said Initial Software.</p><p class="Text_20_body">The Holder undertakes that the Initial Software will remain ruled at least by this Agreement, for the duration set forth in Article <span class="T18">4.2.</span></p><ol><li><ol><li><h class="P24" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__6_2_ON_CONTRIBUTIONS"><span class="T20">6</span>.2 ON CONTRIBUTIONS</a><span class="odfLiEnd"/> </h></li></ol></li></ol><p class="P6"><span class="T1">The Licensee who has developed a Contribution is the owner of the intellectual property rights over it under the conditions defined by the applicable </span><span class="T12">law</span><span class="T1">.</span></p><ol><li><ol><li><h class="P24" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__6_3_JOINT_PROVISIONS"><span class="T20">6</span>.3 <span class="T19">JOINT</span> PROVISIONS</a><span class="odfLiEnd"/> </h></li></ol></li></ol><p class="P6">The Licensee expressly undertakes:</p><ol><li><p class="P14" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">1.</span>not to remove or modify in any way whatsoever the intellectual property notices affixed to the Software;<span class="odfLiEnd"/> </p></li><li><p class="P14" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;">2.</span>to reproduce identically the said intellectual property notices on copies of the Software, modified or not.<span class="odfLiEnd"/> </p></li></ol><p class="P8">The Licensee undertakes not to directly or indirectly infringe the intellectual property rights of the Holder and/or Contributors on the Software and to take, where applicable, vis-à-vis its staff, any and all measures required to ensure respect of said intellectual property rights of the Holder and/or Contributors.</p><ol><li><h class="P22" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_7_-_ASSOCIATE_SERVICES">Article <span class="T21">7</span> - ASSOCIATE SERVICES</a><span class="odfLiEnd"/> </h></li></ol><p class="P2"><span class="T3">7.1 </span><span class="T7">Under no circumstances shall the Agreement oblige the Licensor to provide technical assistance or maintenance services for the Software.</span></p><p class="P3">However, the Licensor is entitled to offer this type of services. The terms and conditions of such technical assistance, and/or such maintenance, shall be set forth in a separate instrument. <span class="T1">These acts of maintenance and/or technical assistance shall engage only the sole responsibility of the Licensor who offers them.</span></p><p class="Text_20_body"><span class="T15">7.2</span> Similarly, any Licensor is entitled to offer to its licensees, under its sole responsibility, a warranty, that shall only be binding upon itself, for the redistribution of the Software and/or the Modified Software, under terms and conditions that it is free to decide. Said warranty, and the financial terms and conditions of its application, shall be subject of a separate instrument executed between the Licensor and the Licensee.</p><ol><li><h class="P22" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_8_–_LIABILITY">Article <span class="T22">8</span> – LIABILITY</a><span class="odfLiEnd"/> </h></li><li><p class="P18" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><span class="T15">8.1</span> Subject to the provisions of Article 8.2, the Licensee shall be entitled to claim compensation for any direct loss it may have suffered from the Software as a result of a fault on the part of the relevant Licensor, subject to providing evidence thereof. <span class="odfLiEnd"/> </p></li></ol><p class="Text_20_body"><span class="T15">8.2</span> The Licensor's liability is limited to the commitments made under this Agreement and shall not be incurred as a result of in particular: (i) loss due the Licensee's total or partial failure to fulfill its obligations, (ii) direct or consequential loss that is suffered by the Licensee due to the use or performance of the Software, and (iii) more generally, any consequential loss. In particular the Parties expressly agree that any or all pecuniary or business loss (i.e. loss of data, loss of profits, operating loss, loss of customers or orders, opportunity cost, any disturbance to business activities) or any or all legal proceedings instituted against the Licensee by a third party, shall constitute consequential loss and shall not provide entitlement to any or all compensation from the Licensor. </p><ol><li><h class="P22" style="margin-left:0cm;"><span style="display:block;float:left;min-width:NaNcm;"><!-- --></span><a id="a__Article_9_-_WARRANTY">Article <span class="T22">9</span> - WARRANTY</a><span class="odfLiEnd"/> </h></li></ol><p class="P1"><span class="T2">9.1</span><span class="T1"> The Licensee acknowledges that the scientific and technical state-of-the-art when the Software was distributed did not enable all possible uses to be tested and verified, nor for the presence of possible defects to be detected. In this respect, the Licensee's attention has been drawn to the risks associated </span><span class="T1">with loading, using, modifying and/or developing and reproducing the Software which are reserved for experienced users.</span></p><p class="Text_20_body">The Licensee shall be responsible for verifying, by any or all means, the suitability of the product for its requirements, its good working order, and for ensuring that it shall not cause damage to either persons or properties. </p><p class="Text_20_body"><a id="good-faith"/><span class="T15">9.2 </span>The Licensor hereby represents, in good faith, that it is entitled to grant all the rights over the Software (including in particular the rights set forth in Article <span class="T26">5</span>).</p><p class="Text_20_body"><span class="T15">9.3</span> The Licensee acknowledges that the Software is supplied "as is" by the Licensor without any other express or tacit warranty, other than that provided for in Article <span class="T26">9.2</span> and, in particular, without any warranty as to its commercial value, its secured, safe, innovative or relevant nature. </p><p class="Text_20_body">Specifically, the Licensor does not warrant that the Software is free from any error, that it will operate without interruption, that it will be compatible with the Licensee's own equipment and software configuration, nor that it will meet the Licensee's requirements. </p><p class="Text_20_body"><span class="T15">9.4</span> The Licensor does not either expressly or tacitly warrant that the Software does not infringe any third party intellectual property right relating to a patent, software or any other property right. Therefore, the Licensor disclaims any and all liability towards the Licensee arising out of any or all proceedings for infringement that may be instituted in respect of the use, modification and redistribution of the Software. Nevertheless, should such proceedings be instituted against the Licensee, the Licensor shall provide it with technical and legal assistance for its defense. Such technical and legal assistance shall be decided on a case-by-case basis between the relevant Licensor and the Licensee pursuant to a memorandum of understanding. The Licensor disclaims any and all liability as regards the Licensee's use of the name of the Software. 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Axon command-line runner (``axon-runprocess``) allows to enable/disable pipeline nodes

More complete support for GLTF 3D scenes format in Anatomist and AIMS libraries

Fixes in ROI/label volume edition, which could involve data loss.

Fixes and improvements under the hood in AIMS / PyAIMS libraries.

Brainvisa switches back to using an older API to display HTML docs because it could cause crashes on old linux systems (even inside a container)

This containerized release is based on an Ubuntu 22.04 system, and compiled for Python 3.10 and Qt 5. This is thus the first official binary release based on Python3 (yes, finally...)

This containerized release is based on an Ubuntu 22.04 system, and compiled for Python 3.10 and Qt 5. This is thus the first official binary release based on Python3 (yes, finally…)

It also ships a copy of SPM12-standalone, preconfigured in Axon (brainvisa) in order to work out-of-the-box without user configuration.

Towards BIDS compatibility: Morphologist (in Axon and Capsul) can now support a new BIDS-compatible ontology. The Freesurfer toolbox also supports a new BIDS-like ontology.

Several significant news in Anatomist, see :anatomist:`Anatomist changelog <user_doc/changelog.html>`

The image processing libraries (AIMS/PyAIMS) have been cleaned from some obsolete data structure, and improved in several ways. Some old commands (Vip) have also been removed when existing in a newer shape.

Very important performance improvements in Soma-Workflow, the parallel execution tool.

The SnapBase tool, which had not been maintained for years, has been removed.

Morphologist: the CNN sulci recognition could produce (in rare bad cases) both sulcus vertices with disconnected voxels, and adjacent cut vertices with the same label (which was not severe but useless). This has been reworked and fixed. As a consequence, the outputs of CNN sulci recognition are different in 5.1 and 5.0.

Minor improvements, and many fixes in both infrastructure and toolboxes.

Fixes in Aims libraries (Mesher, AimsRegisterFFDEstimate, AimsTex2Vol)

Fixes in Anatomist: crash in Fusion3D using more than 2 volumes, folds split, CutMesh referentials issue, ...

Fixes in Anatomist: crash in Fusion3D using more than 2 volumes, folds split, CutMesh referentials issue, …

unable to read Nifti files whose name is shorter than 7 characters.

all commands fail to start with nvidia-container-cli: initialization error: nvml error: driver not loaded.

Uncatched exceptions that occurs in BrainVISA lead to a crash of the application

Opening Graph file by clicking the "eye" button crashes BrainVISA

Opening Graph file by clicking the “eye” button crashes BrainVISA

Brings a new installation method as virtual containers or virtual machines.

Morphologist sulci identification is using a new method (based on deep learning CNNs)

Fixes a number of issues, including the broken Mac package. Most other are relatively small fixes and improvements.

Anatomist:

* Allow to put independently several volumes in the same window: a fusion will be created on-the-fly
* New little image "math" module

Allow to put independently several volumes in the same window: a fusion will be created on-the-fly

The Constellation toolbox has still not been finished for this release.

General:

* Windows version has been fixed
* Windows 64 bits version
* Stopped the Fedora-4 32 bits version. All linux builds are in 64 bits.

Stopped the Fedora-4 32 bits version. All linux builds are in 64 bits.

* Supports object of any dimensionality (not limited to 4D any longer)
* Partial support for CIFTI connectivity matrices
* New referentials window, rewritten in 3D
* Windows snapshots of any dimension, rendered off-screen
* Save/reload fusion objects and multiple objects (.aobj format)
* Display normals of a mesh
* Display vector fields
* Many other fixes and smaller improvements

Supports object of any dimensionality (not limited to 4D any longer)

New project: :axon:`Primatologist <en/processes/categories/primatologist/category_documentation.html>`
Which is part of the BrainRat project from Mircen BioPicsel lab.

Coming soon

* :axon:`Constellation <en/processes/categories/constellation/category_documentation.html>`, the connectivity-based parcellation toolbox for BrainVisa, is still a bit delayed because of recent changes, and to allow us to ship an atlas with it. We hope it will be released soon, before a full new brainvisa release.
* Highres-Cortex, :hr_cortex:`See the doc <doxygen/index.html>`. As for
Constellation the release will be delayed a little bit.

:axon:`Constellation <en/processes/categories/constellation/category_documentation.html>`, the connectivity-based parcellation toolbox for BrainVisa, is still a bit delayed because of recent changes, and to allow us to ship an atlas with it. We hope it will be released soon, before a full new brainvisa release.

, the connectivity-based parcellation toolbox for BrainVisa, is still a bit delayed because of recent changes, and to allow us to ship an atlas with it. We hope it will be released soon, before a full new brainvisa release.

Highres-Cortex, :hr_cortex:`See the doc <doxygen/index.html>`. As for

Removed obsolete toolbox Connectomist-1

This toolbox was almost unmaintained for about 10 years. Parts still useful have been integrated in the :aimsusr:`AIMS <index.html>` library, and in :axon:`Constellation <en/processes/categories/constellation/category_documentation.html>`

This toolbox was almost unmaintained for about 10 years. Parts still useful have been integrated in the 

Notably nothing important in :axon:`Morphologist <en/processes/categories/morphologist/category_documentation.html>`... a few minor improvements in :morphouiusr:`morphologist UI <index.html>`

For developers:

* Ported all libraries to Qt5 or Qt4
* Support for python3 in a subset of projects (noticeably excluding Axon)
* Support for C++11 in all C++ libraries, also compiles using LLVM compiler
* :capsul:`Capsul <index.html>` has notably improved and matured, integration in Axon has also improved (although it is not entirely integrated yet)
* New development and build system in Docker containers: :casadistro:`casa-distro project <index.html>`

Support for python3 in a subset of projects (noticeably excluding Axon)

Support for C++11 in all C++ libraries, also compiles using LLVM compiler

:capsul:`Capsul <index.html>` has notably improved and matured, integration in Axon has also improved (although it is not entirely integrated yet)

 has notably improved and matured, integration in Axon has also improved (although it is not entirely integrated yet)

New development and build system in Docker containers: :casadistro:`casa-distro project <index.html>`

Morphologist:

* Imporoved meshes.
* Additional optional step to skull-strip the brain and use it in a second normalization step, to improve alignment robustness.
* A variant of the pipeline is the premise to the future redesigned pipelining system (Capsul): "Morphologist CAPSUL iteration". It should behave the same way, but preparing a large iteration on many subjects should be more efficient and faster. The process produces a workflow, to be run in :soma_workflow:`soma_workflow_gui <gui.html>`

Additional optional step to skull-strip the brain and use it in a second normalization step, to improve alignment robustness.

A variant of the pipeline is the premise to the future redesigned pipelining system (Capsul): "Morphologist CAPSUL iteration". It should behave the same way, but preparing a large iteration on many subjects should be more efficient and faster. The process produces a workflow, to be run in :soma_workflow:`soma_workflow_gui <gui.html>`

A variant of the pipeline is the premise to the future redesigned pipelining system (Capsul): “Morphologist CAPSUL iteration”. It should behave the same way, but preparing a large iteration on many subjects should be more efficient and faster. The process produces a workflow, to be run in 

**Morphologist UI**: a new simplified interface to the Morphologist pipeline.
See :morphouiusr:`the documentation <index.html>`

Cortical_surface:

* New sulcus parameterization, faster, more robust, better properties.
* Improved version of the Hip-Hop cortical parameterization process
* The MarsAtlas cortical parcellation model has arrived !
* Sulcal pits computation for individual subjects.See in Anatomy section.
* The Depth Potential Function (DPF) computation is now included in the Anatomy / tools section

New sulcus parameterization, faster, more robust, better properties.

Improved version of the Hip-Hop cortical parameterization process

Sulcal pits computation for individual subjects.See in Anatomy section.

The Depth Potential Function (DPF) computation is now included in the Anatomy / tools section

* Supports Wavefront .obj format
* Supports NIFTI-2 format
* Supports Trackvis .trk format
* Can save and reload textured meshes with colormap (as .obj), especially convenient to import/export with other software like Blender.
* Shader-based rendering of fibers, with coloring
* Major improvements in SurfPaint module
* Improvements in transparent objects rendering (possibility to sort polygons)

Can save and reload textured meshes with colormap (as .obj), especially convenient to import/export with other software like Blender.

Improvements in transparent objects rendering (possibility to sort polygons)

<!doctype public "-//w3c//dtd html 4.01 transitional//en"
		"http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
   <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
   <title>Anatomist/BrainVISA changelog</title>
    <link href="bvstyle.css" rel="stylesheet" type="text/css">
</head>
<body bgcolor="#FFFFFF">

<a name="2013_11_18"></a>
<h3 class="news">November 18th, 2013, New BrainVISA release: version 4.4.0</h3>
<p>This version allows a more incremental management of databases, allowing incremental updates after distributed computing. A new database organization (fully compatible with the previous one) is also provided. Many graphical and practical improvements have also been added, in addition to "traditional" bug fixes. See the <a href="doc/axon/en/help/changelog.html">Axon detailed changelog</a>.<p>
<p>Anatomist has also undergone some important improvements, in graphical interactions, as well as some new objects types. See <a href="doc/anatomist/html/en/changelog.html">Anatomisr detailed changelog</a></p>
<p>Morphologist provides a reorganized pipeline, and improvements in meshes.</p>
<p>Amongst noticeable changes, the <a href="http://www.meca-brain.org/softwares/">Cortical surface toolbox</a> (LSIS/CNRS, Marseille) has also been significantly improved.
</p>
<p><b>New:</b> (2013/11/18) <a href="https://trac.int.univ-amu.fr/vobi_one">Vobi One</a>, a new toolbox for functional optical imaging, has just been released by the INT/CRNS in Marseille. See the <a href="toolboxes.html">toolboxes page</a>, or the <a href="https://trac.int.univ-amu.fr/vobi_one">dedicated web site</a>.</p>

<a name="2012_09_06"></a>
<h3 class="news">September 6th, 2012 New BrainVISA release: version 4.3.0</h3>
<p>In this version, it is possible to store <b>history</b> information about output data generated by Brainvisa processes. History management can be activated for a database through its <i>expert settings activate_history</i> option. History of data can be consulted via the <a href="doc/axon/user_doc/axon_manual2.html#database-browser">Database browser</a>.</p>
<p>This version also brings a number of bug fixes, and improvements:</p>
<ul>
<li><p><b>BrainVISA</b> (See <a href="doc/axon/en/help/changelog.html">detailed changelog</a>)</p></li>
<ul>
<li>Information message when a <b>new version of Brainvisa</b> is available on http://brainvisa.info</li>
<li>Invalid processes are not hidden anymore</li>
<li>The <b>documentation panel</b> in Brainvisa main window is now a real web browser.</li>
<li><b>Reusable Anatomist windows in Brainvisa</b></li>
<li>New feature in menu <i><b>View -&gt; Close all viewers</b></i></li>
<li><p><b>Important changes for developers:</b></p>
<ul>
<li><b>Anatomist in "direct" mode:</b> this change allows more sophisticated viewers (BV/Anatomist combined interfaces)</li>
<li>Reorganization of Brainvisa python modules</li>
</ul>
</li>
<li><p><b>Morphologist toolbox</b></p>
<ul>
<li>The T1 MRI, Sulci and Morphometry toolboxes are now grouped together into the <b>Morphologist</b> toolbox.</li>
<li><b>Snapbase:</b> a new tool to do large scale snapshots of data from Brainvisa databases.</li>
<li>Fix an incorrect flip in Prepare subject step in a specific orientation.</li>
</ul>
</li>
</ul>
<li><p><b>Anatomist</b> (See <a href="doc/anatomist/html/en/changelog.html">detailed changelog</a>)</p></li>
<ul>
<li>New <b>2D fusion</b> modes</li>
<li>Fix visibility of icons in menus</li>
<li>Fix closing mode in ROI toolbox</li>
<li>Fix to enable displaying huge images</li>
<li>The <i>Clear everything</i> menu can really close all windows now</li>
<li>The matplotlib-histogram window has been improved, and is now the default histogram window</li>
<li>The manual sulci splitting plugin has been significantly improved</li>
<li>Graph labels display as text in 3D</li>
<li>Anatomist windows highlighting</li>
<li>Optimizations in huge nomenclature / graphs coloring</li>
<li>Use the Qt4 file dialog</li>
</ul>

<li><p><b>Aims</b> (See <a href="doc/aimsdata/html/en/changelog.html">detailed changelog</a>)</p></li>
<ul>
<li>AimsVoiStat command is now deprecated, <b>AimsRoiFeatures</b> command should be used instead</li>
<li>It is now possible to use volumes whose size is larger than 32 bits.</li>
<li>Fix in AimsFoldArgAtt command</li>
<li>Fix in fold split</li>
<li>Fix operators on volumes in PyAims</li>
</ul>

</ul>

<a name="2012_02_16"></a>
<h3 class="news">February 16th, 2012 bugfix update: version 4.2.1</h3>
<p>This version brings a few bug fixes, and improvements:
<li>Fix a problem with referentials and transformations in Brainvisa databases.</li>
<li>Fix SPM configuration in Brainvisa preferences. </li>
<li>Fixes in Soma-workflow integration in Brainvisa. </li>
<li>Fixes in Morphologist pipeline.</li>
<li>Fix translations in Anatomist.</li>
</p>

<a name="2012_02_03"></a>
<h3 class="news">February 3rd, 2012, New BrainVISA release: version 4.2.0</h3>
<p>In this version, it is very easy to do <b>parallel computing</b> in BrainVISA. Indeed, <a href="http://brainvisa.info/soma/soma-workflow/">Soma-workflow</a> has now been completely integrated in BrainVisa: processes (pipelines) may be run through a "Run in parallel" button, which allows to dispatch processing across local processors, or on a remote computing resource. A specific GUI allows to control and monitor all executions. Change the user level to <i>Advanced</i> or more in BrainVISA preferences to use this new feature. More information in the <a href="doc/axon/user_doc/axon_manual2.html#distributing-an-iteration-on-a-multi-core-machine">BrainVISA manual</a>.</p>
<p>A new toolbox for Freesurfer is also proposed (user level 1). Some data such as segmentation cortex (ribbon.mgz) can be imported into brainvisa databases and  cortical fold graph can be extracted from this freesurfer segmentation.</p>
<p>This version also brings a number of bug fixes and improvements:</p>
<ul>
<li><b>BrainVISA</b> (See <a href="doc/axon/en/help/changelog.html">detailed changelog</a>)</li>
  <ul>
    <li>GUI changes in BrainVisa main window</li>
    <li>Transformations manager performance improvements</li>
    <li>"Reload toolboxes" option in BrainVISA menu</li>
    <li>Processes and iterations numbering improvement</li>
    <li>New <b>data lock</b> feature</li>
    <li>New process InspectMultipleData in data management</li>
    <li>Fixed environment variables when using external commands from brainvisa.</li>
    <li>Fixes in file selection of a list of output files.</li>
    <li><b>T1 MRI toolbox</b></li>
      <ul>
      <li>Support for SPM8 and SPM8 compiled version for normalization process</li>
      <li>Hemisphere and white meshes are now more accurate, prettier, and conform to the spherical topology constraint.</li>
      <li>SPM and FSL normalization processes can retry after a failure due to a bad initialization</li>
      </ul>
    <li><b>Sulci toolbox</b></li>
      <ul>
        <li>SPAM sulci recognition models data have been reorganized.</li>
        <li>SPAM models viewers have been improved and a bad interaction with other objects in anatomist has been fixed.</li>
      </ul>
    <li><b>FreeSurfer toolbox</b></li>
      <ul>
        <li>A process to import the freesurfer segmentation (ribbon.mgz) and to extract cortical fold graph from this segmentation (and not this computed by Morphologist pipeline (user level 1).</li>
        <li>Many processes under development in user level 2. These processes are unstable, so if you want to try them, please remenber that ...</li>
      </ul>
  </ul>
<li><b>Anatomist</b> (See <a href="doc/anatomist/html/en/changelog.html">detailed changelog</a>)</li>
  <ul>
  <li>Box selection highligting feature</li>
  <li>Fixes and improvements in browser window</li>
  <li>Windows blocks improvements</li>
  <li>New config option: <tt>commonScannerBasedReferential</tt>. When enabled, all such referentials found in image headers are assumed to be the same.</li>
  <li>Surfpaint module update</li>
  <li>New palettes: "Graph-Label", "pastel-256", "French"</li>
  <li>Fixes and improvements about referentials and transformations</li>
  <li><b>Fixed multi-texturing bug on Windows OS</b></li>
  </ul>
<li><b>Aims</b> (See <a href="doc/aimsdata/html/en/changelog.html">detailed changelog</a>)</li>
  <ul>
  <li>Geodesicpath library update</li>
  <li>DICOM reader fixes for a few header fields, and support for SPECT data.</li>
  <li>Fixed rescaling in volume converters</li>
  <li>Fixed a bug in SplineResampler</li>
  </ul>
</ul>

<p>The package includes <a href="http://brainvisa.info/soma/soma-workflow/">Soma-workflow 2.1</a>.</p>

<a name="2011_09_14"></a>
<h3 class="news">September 14th, 2011, Bug fix update: version 4.1.1</h3>
<p>This version brings a number of bug fixes, and minor improvements:</p>
<ul>
<li>BrainVISA</li>
  <ul>
  <li>Updated tutorial available</li>
  <li>Fix the field "defined in file" in the Brainvisa ontology documentation.</li>
  <li>Brainvisa Python API documentation in sphinx format available.</li>
  <li>New supported mesh format: MNI .obj</li>
  <li>Fix generic importation of a graph in basic user level mode.</li>
  <li>Fix concurrent creation of a directory in case of parallel executions of Brainvisa.</li>
  <li>New python module to start Brainvisa in batch mode: <i>brainvisa.axon</i>.</li>
  </ul>
<li>Anatomist</li>
  <ul>
  <li>New rotation mode where we don't need to keep the middle mouse button down: it is now possible to rotate an object by performing a double click with the middle button and moving the mouse. Another click ends this special rotating mode.</li>
  <li>New Text objects to display text information in Anatomist windows.</li>
  <li>More python bindings in the Python API.</li>
  </ul>
<li>Morphologist toolbox</li>
  <ul>
  <li>Fix missing step in graph upgrade process.</li>
  <li>Fix wrong link in Cortical fols graph process.</li>
  <li>Fix a bug in the closing option of VipGetHead command.</li>
  </ul>
</ul>
<p>The package includes <a href="http://brainvisa.info/soma/soma-workflow/">Soma-workflow 2.0</a>.</p>

<a name="2011_05_17"></a>
<h3 class="news">May 17th, 2011, New BrainVISA release: version 4.1.0</h3>
<p>In this version, an important change for the developers should be noted : the build tool used to compile from the source code has changed. We dropped our home-made tool <i>build-config</i> and replaced it with the standard tool <a href="http://www.cmake.org/">CMake</a>, a cross-platform, open-source build system.
</p>
<p>This new package compiled with CMake doesn't need an installation step anymore. You just have to download it and uncompress the archive, then it is ready to use. Thus, there is no setup script or program anymore. The <i>cartopack.sh</i> script that used to add the package paths in environment variables have been renamed into bv_env.sh.</p>
<p></p>
<p>The package includes a new tool that helps submitting parallel computing to various computing resources: <b>soma-workflow</b>. The documentation is <a href="http://brainvisa.info/soma/soma-workflow/">here</a>.</p>
<p></p>
<p>This version also brings a number of bug fixes, and improvements:
</p>
<ul>
<li><b>BrainVISA</b></li>
<ul>
<li>Text search available in the log throught ctrl+F and F3 keys</li>
<li>Text viewer available for more data types (csv, xml files).</li>
<li>[programmers] Brainvisa now uses sip QString API version 2, so it not possible to use QString and QStringList classes anymore, python types should be used instead.</li>
<li>Fix graphviz packaging which make generation of ontology documentation with types inheritance graphs available.</li>
<li>Update in programming documentation about GUI customization</li>
<li><b>T1 MRI toolbox</b></li>
  <ul>
    <li>New T1 pipeline named <b>Morphologist</b>. This new version is more robust and efficient.</li>
    <li>T1 Normalization processes (using FSL or SPM) have been moved from fMRI to T1MRI toolbox. So, it is now possible to choose normalization instead of manual localization of AC/PC in the anatomical pipeline without having the fMRI toolbox installed.</li>
  </ul>
<li><b>Sulci toolbox</b></li>
  <ul>
    <li>New process <b>SPAM models installation</b> to install SPAM models for sulci recognition. The installation of the required models is checked in the Morphologist pipeline.</li>
    <li>Add new 2011 ANN models to sulci recognition available models. These models implement the older method, on the same (newer) learning database as the one used for SPAM models.</li>
    <li>Bug fix in iterative mode of a sulci graph viewer</li>
  </ul>
<!-- li>New toolbox <b>Optical Imaging</b></li-->
<li><b>BrainRAT toolbox</b></li>
  <ul>
    <li>Add RGB/RGBA background estimation to subsampling and to intra volume registration process</li>
    <li>Add advanced slice replacement process</li>
  </ul>
</ul>

<li><b>Anatomist</b></li>
<ul>
<li>New <b>surfacic ROI drawing toolbox</b>: it is now possible to paint on a mesh (into a texture), and use curve drawing tools which include curvature constraints. This toolbox is developed in Marseille by O. Coulon's team, mainly by A. Le Troter.
</li>
<li>Update and additions to pyanatomist documentation.</li>
<li>Bug fix in FusionRGBAVolumeMethod fusion method</li>
<li>Bug fix in palette update in a MultiTexture fusion</li>
</ul>

<li><b>Aims</b></li>
<ul>
<li>Add support for RGB/RGBA background in AimsResample</li>
<li>PyAims</li>
  <ul>
    <li>Bug fix in aims.write when the specified path doesn't exist.</li>
    <li>Helper functions to create the main Aims data types</li>
    <li>Allow additional constructors arguments for volumes and textures (build from another volume, or a numpy array...)</li>
    <li>Big fix in TimeSurface erase function</li>
  </ul>
</ul>

</ul>

<a name="2010_11_22"></a>
<h3 class="news">November 22nd, 2010 bugfix update: version 4.0.2</h3>
<p>This version brings a number of bug fixes, and improvements:
</p>
<ul>
<ul>
<li>New progress bar in processes and pipeline windows.</li>
<li>Viewers and Editors are now available for list of data. The default viewer is an iteration of the viewer for the type of data in the list.</li>
<li>Fix background and foreground color of choice nodes in pipeline graphical interface.</li>
<li>Fix iteration on Series of 3D volume (Import fMRI data)</li>
<li><b>Database browser</b>: enable visualization of unrecognized data if a viewer that accepts the data format exists.</li>
<li>Fix commands log in windows version.</li>
<li>Documentation panel : enable links with anchor and open web links in a real web browser when possible.</li>
<li>Browse button in process iteration dialog always opens the dialog that enables selecting several files at different location on the filesystem.
This action was only available through right click before.</li>
<li>Improvement of database update when a process finishes : intermediate directory items created by the process are inserted in the database;
output parameters of a sub-process not in a pipeline are inserted in the database. </li>
<li>Improvement in <b>Morphometry statistics</b> process : output parameters are now output_directory and output_filename_prefix instead of output_prefix and have default values.</li>
<li>Improvement in <b>DicomToNiftiConverter</b> process : enable choosing the output filename and giving a directory containing dicom images instead of a file as input parameter.</li>
<li>New importation process to import a T1 MRI from a Dicom directory using Mricron Dicom converter.</li>
<li>Fix <b>Single file to serie</b> process : generate the numbers of the serie with a fix number of digit to ensure that the files of the serie are in the correct order.</li>
<li><b>T1 MRI</b> : new sulci voronoi step before the folds thickness step, to allow saving and reusing the sulci voronoi maps; New type for lesion mask used in the brain segmentation parameters.</li>
<li><b>Sulci</b> : new processes to calculate the mean distance from a lesion mask to sulci.</li>
</ul>
<ul>
<li>New option in Anatomist config and preferences panel: <tt>clipBrowserValues</tt>. This option allows to limit the size of strings displayed in browsers attributes, and avoid crashes due (probably) to too large pixmaps in X servers in some specific cases.
</li>
<li>Gradient palette available for RGB images.</li>
<li>Improvement of tooltips on graphs in "display property" mode</li>
<li>Fix rendering problems using ATI cards and drivers on S16 volumes.</li>
<li>Fix ROI cursor display</li>
</ul>
<ul>
<li>Fix reading GIFTI files extracted from SPM 8 and GIFTI mesh+texture files</li>
<li>Fix reading and writing transformations in MINC format</li>
<li>Support for MNI .obj mesh format</li>
<li>Forbids to write NIFTI format when volume dimensions do not fit in short ints: NIFTI stores dimensions as short.</li>
<li>New option in AimsFileConvert: --orient, to specify output disk orientation or flip it</li>
<li>AimsFoldGraphThickness can now use a pre-built sulci voronoi map (to speed things up)</li>
<li>AimsLabelSelector can now work in batch mode (-b) without graphical interface.</li>
</ul>

</ul>

</ul>

<a name="2010_08_02"></a>
<h3 class="news">August 2nd, 2010 bugfix update: version 4.0.1</h3>
<p>This version brings a number of bug fixes, and minor improvements:
</p>
<ul>
<li>New Dicom converter using Mricron. The converter is in toolbox tools -&gt; converters. It is available if Mricron is installed on your computer.</li>
<li>Fix database conversion process which was not compatible with qt4.</li>
<li>Fix BrainVISA log file.</li>
<li><b>Cortical surface</b>: Fix gyral parcellation (command siParcellation). </li>
<li><b>T1 MRI pipeline</b>: test if brain mask is empty or full and fail accordingly</li>
<li><b>Sulci</b>: Fix scripts siCSVMapGraph, siDiffModels, siDisplayGraph and annealing_tag which were not compatible with qt4.</li>
<li><b>Anatomist</b>: graph labels picking/copy/paste from one window to another is now possible.</li>
<li><b>BrainRAT</b>:</li>
<ul>
<li>Fix issue in intra volume propagative slice registration</li>
<li>Fix command AimsFFDApply</li>
<li>Add AimsFlip RGB support</li>
<li>Add a variation ratio parameter to AimsIndividSlices</li>
<li>Add RGB support to FlipApplication</li>
<li>Add threshold parameter to IntraVolumePropagativeSliceRegistration process</li>
<li>Fix issue in AimsIndividStackSlices and AimsIndividSlices</li>
</ul>

</ul>

<a name="2010_07_22"></a>
<h3 class="news">July 22th, 2010, New version of BrainVISA fMRI toolbox : 4.0</h3>
<p>The 4.0 release of the fmri toolbox comprises the following new features:</p>
<ul>
<li>Improved and more robust cortical surface-based analysis procedures.</li>
<li>Improvements in multi-subjects analysis, such as the introduction of second-level design matrices.</li>
<li>Better integration of General Linear Model in the volume and on the surface with high-level operations (group analysis, reproducibilitry assessement, parcellation and functional landmark characterization).</li>
</ul>
<p>It is compatible with BrainVISA 4.0.</p>

<a name="2010_06_15"></a>
<h3 class="news">June 15th, 2010, New version 4.0</h3>
This is the first version of BrainVISA using Qt4 API. Be careful, Qt4 API is quite different from Qt3. If some of your own processes use Qt, you may have to port them to Qt4 (See <a href="http://doc.trolltech.com/4.6/porting4.html">Porting to Qt 4</a> on Qt documentation pages). This version's source code is still compatible with Qt3, so if you compile from source, you can still use Qt3. Note that the compatibility will not be guaranteed anymore in BrainVISA 4.1.
</p>
<p>This new version also brings a lot of bug fixes and some improvements in user interface:</p>

<ul>
  <li>BrainVISA</li>
  <ul>
<li>New contextual menu on pipelines and iterations enabling easy selection, deselection, opening and documentation display of the different steps.</li>
<li>Visual feedback in processes graphical interface to show which parameters have been modified.</li>
<li>BrainVISA documentation panel: keyboard shortcuts for contextual menu items and a new button to reload the current documentation page. </li>
<li>Attributes sorting enabled in database search interface (available only in Qt4 version).</li>
<li><b>Import T1 MRI</b>: the default value for subject attribute is the name of the file.</li>
<li>Types and formats documentation now shows the hierarchy rules for all available ontologies</li>
<li>Fix: parameter exactType in WriteDiskItem initialization is now taken into account.</li>
<li><b>Sulci toolbox</b> - ergonomy improvements in Sulci recognition pipeline: combo boxes to select the recognition method.</li>
  </ul>
    <li>Anatomist</li>
  <ul>
<li>OpenGL-based selection infrastructure. Selection functions for meshes and polygons have been included in Anatomist. In "debugger" mode (userLevel &gt;= 3) this mode replaces the older graph/bucket selection mechanism. When correctly tested, it will fully replace it.<br/>
A little texture drawing code example is now part of the examples.<br/>
The new infrastructure is not optimized at all yet, so, drawing is slow, but we will improve it in time to avoid unnecessary OpenGL renderings.
</li>
<li>Python bindings and the python API have been slightly improved.</li>
<li>New command: ApplyBuiltinReferential</li>
<li>The file browser for loading objects now shows all file extensions used by supported objects files. Extensions list is built dynamically from the loaded readers.
</li>
<li>Clearer tooltips in the referentials window.</li>
<li>Many problems have been fixed when Anatomist is built using Qt4. Some modules had not been ported or tested, and Mac and Windows ports had not been tried. Now things are mostly tested.
</li>
</ul>
<li>AIMS</li>
<ul>
<li>Improvements and fixes in various IO modules: Dicom, Nifti, Gifti, FDF
</li>
<li>Beginning of a SQL database format for graphs (QSlite files for now). This will allow partial reading and queries in large graphs databases. But the module is still experimental and the SQL database schema will probably change, so it should not be used yet to store important graphs. Conversion from and to the .arg format are still possible.
</li>
</ul>
</ul>

<a name="2010_01_27"></a>
<h3 class="news">January 27, 2010, bugfix update: version 3.2.1</h3>
<p>This version brings, as usual, a number of bug fixes, and minor improvements. A few noticeable changes also:
</p>

<ul>
  <li>Binary packages</li>
  <ul>
    <li>
      Something we just forgot to mention but was already present in version 3.2: Linux packages include a <b>software OpenGL library</b> (Mesa) which may be used in place of the system one in case of 3D drivers rendering problems. To enable it, just move the files in &lt;cartopack_directory&gt;/lib/mesa/ into &lt;cartopack_directory&gt;/lib/ and re-run Anatomist/BrainVisa. It is slow because it does not make use of the 3D hardware at all, but should work and display correctly in all cases. Only use it if the system OpenGL does not work well.
    </li>
    <li>A few system libraries have been added to the binary distribution to overcome compatibility problems on some systems.
    </li>
    <li>The <b>fMRI toolbox</b> will also be released for the Linux Mandriva 2008 x86_64 (<b>64 bits</b>) version.
    </li>
  </ul>
  <ul>
    <li>A serious bug has been fixed on the <b>database system on Windows</b>, it fully made the database unusable in 3.2 version (on Windows). It is now fixed.
    </li>
    <li>
      <b>T1 pipeline:</b> the pipeline can now make use of the spatial normalization processes of the fMRI toolbox to replace the manual AC/PC clicking step. To make it available, you need to have the fMRI toolbox installed, and also have either FSL or SPM5 (+ Matlab) installed and present in the PATH. As the fMRI toolbox is only released for Linux, you will not be able to have it on Mac and Windows (unless you install the sources of the toolbox, actually at least the FSL normalization does work on Mac).
    </li>
    <li>
      <b>Sulci recognition:</b> The various and more advanced sulci recognition methods of Matthieu Perrot's PhD work have now been released. They need to install additional models archives. See the docs of the SPAM-based recognition processes.
    </li>
    <li>A few little improvements to make database and T1 import processes more practical.
    </li>
  </ul>
  <li>Anatomist</li>
  <ul>
    <li>
      A new <b>simplified viewer application</b> has been developed: <b>anasimpleviewer.py</b>. It offers a simple and easy interface in a single window using a fixed 4-views layout, which is more classical and more convenient for inexperienced users. It is a restricted and constrained use of Anatomist capabilities. It has been developed in a few nights, at first to show that developing simple custom applications using Anatomist libraries is not so difficult and may be done quite fast in Python language...
    </li>
    <li>
      A new plugin allows to <b>tune the palette (contrasts)</b> of objects using the mouse right button (+ shift/control keys) directly on 2D/3D views without opening the palette window.
    </li>
    <li>
      A better <b>histogram window</b> plugin, based on <a href="http://matplotlib.sourceforge.net/">Matplotlib</a>, which offers interactivity (zooming, saving/snapshot in either bitmap or vector formats, ...)
    </li>
    <li>The ROI drawing cursor hs been fixed and re-activated on Mac
    </li>
  </ul>
</ul>

<a name="2009_11_05"></a>
<h3 class="news">November 05, 2009, New BrainVISA release: version 3.2.0 </h3>
<p>This new release is mainly due to internal changes and reorganization of our sources repository. This sources repository and web interface for bug tracking are now accessible for open-source parts to contributors. See <a href="../repository.html">this page</a> for details.</p><p>This release also brings many bug fixes and improvements : </p>

<ul>
<li>Binary Packages</li>
<ul>
<li>The windows version should work on <b>Windows Vista</b>.</li>
<li>A <b>64 bits</b> binary package is now available for Linux.</li>
<li>The Mac version is now built on an Intel machine. It is <b>no longer compatible with PPC processors</b>, but it should run way faster on Intel Macs.
</ul>
<ul>
<li><b>Several improvements on BrainVISA databases</b> : </li>
<ul><li>Optimization of databases requests. The results are now shown as a table of attributes values.</li>
<li>Easier database request with existing values of databases attributes selectable</li>
<li>Databases can be moved without needing update.</li>
</ul>
<li>DiskItem selection window cannot become higher than screen anymore</li>
<li>No more useless *.minf created by processes</li>
<li>Iteration control : it is possible to stop the current iteration or all iterations.</li>
</ul>
<ul>
<li><b>VTK plugin</b> by Pierre Fillard, which allows to render VTK objects, and especially enables a mix between Anatomist and <a href="http://www-sop.inria.fr/asclepios/software/MedINRIA/">MedInria</a> objects.
</li>
<li><b>GIFTI</b> format IO support for meshes and textures</li>
</ul>
</ul>

<a name="2009_07_24"></a>
<h4 class="news">July 24, 2009, fMRI toolbox for BrainVISA update: version 3.1.6.1</h4>
<p> This release brings small bug fixes, and introduces python-nifti IO library.
<a href="fmri_tbx.html">More info</a>
</p>

<a name="2009_05_19"></a>
<h4 class="news">May 19, 2009, fMRI toolbox for BrainVISA update: version 3.1.6</h4>
<p> This release brings brand new group analysis processes. It also
  corrects some bugs and allows a better gestion of the analysis models. <a href="fmri_tbx.html">More info</a>
</p>

<a name="2009_05_15"></a>
<h4 class="news">May 15, 2009, bugfix update: version 3.1.6</h4>
<p>This update brings more bug corrections and improvements. It includes more recent versions of Numpy (1.3.0) and Scipy (0.7.0). The Windows package now uses Python 2.5 like the Linux and MacOs packages.</p>

<li>Fixes in BrainVISA: toolboxes can now completely define new ontologies; Suppressed a latency when clicking the "run" button of a process</li>
<li>Fixes and improvement in T1MRI toolbox: PrepareSubject process now handles all orientations; <b>new TalairachTransformationFromNormalization process</b> to import orientation parameters from a normalization file...</li>
<li>Improvements in Sulci toolbox: <b>new multi-subject sulci snapshot process</b> and <b>new sulci labels transfer process</b> to transfer a labeling to another sulci graph with a different segmentation and graph structure (but same subject)...</li>
<li>Fixes and improvements in Anatomist: fix coronal and sagittal views orientation in direct referentials, some objects update functions, "clear unused referentials" feature; new ClippedObject, allowing to cut any object by a clipping plane with its own orientation... </li>

<a name="2009_03_03"></a>

<h4 class="news">March 03, 2009, fMRI toolbox for BrainVISA release: version 3.1</h4>
<p> This toolbox was once a part of the BrainVISA and now is an
  independant toolbox. <a href="fmri_tbx.html">More info</a>
</p>

<a name="2009_02_20"></a>

<h4 class="news">February 20, 2009, bugfix update: version 3.1.5</h4>
<p>This update brings more bug corrections and improvements.</p>

<li>Improvement of processes documentation : each data type mentionned in a documentation is a link to a detailed documentation about the data type (inheritance, processes that use it, associated formats, place in Brainvisa databases). The source code of a process can now be displayed in the browser.</li>
<li>Bug about process parameters default values.</li>
<li>More data types and formats accepted in some processes. Now, it is possible to make the anatomical pipeline generate all the outputs in nifti format for example.</li>
<li>Application Qt style can now be changed from BrainVISA configuration panel</li>
<li>In databases configuration, ontologies list is not hard-coded anymore</li>
<li>Improvement and bug fixes in anatomist python api.</li>
<li>A new sulci recognition method is available in BrainVISA : it is faster and behaves differently. It is available as an alternative method in the T1 pipeline.</li>

<a name="2008_11_14"></a>

<h4 class="news">November 14, 2008, bugfix update: version 3.1.4</h4>
<p>This update brings more bug corrections and optimization.</p>
<p>This package is distributed with the new <a href="toolboxes.html">BrainRAT <img src="images/brainrat/brainrat.png" border="0" style="position:relative;top:3px"></a> toolbox dedicated to ex-vivo 3D reconstruction and analysis.
</p>
<p>Starting with BrainVISA 3.1.4, the <a href="toolboxes.html">fMRI toolbox</a> will be distributed separately as a downloadable add-on package to provide it its own visibility.
</p>

<a name="2008_10_03"></a>

<h4 class="news">October 3, 2008, bugfix update: version 3.1.3</h4>
<p>This update brings more bug corrections and optimization of database access. This package is distributed with a more recent sqlite library.
</p>

<a name="2008_09_03"></a>

<h4 class="news">September 3, 2008, bugfix update: version 3.1.2</h4>
<p>This update brings more bug corrections, including some database importation problems fixes.
</p>
<p>In Anatomist, a noticeable improvement is the presence of a new gradient palette edition module which may be quite useful.
</p>

<a name="2008_08_07"></a>

<h4 class="news">August 7, 2008, bugfix update: version 3.1.1</h4>
<p>A number of bugs have been fixed since brainvisa/anatomist 3.1 have been released, so a new package is now available.
</p>

<a name="2008_05_10"></a>
<h4>June 9, 2008, new release: version 3.1</h4>
<p>Finally, a new release, after about 3 years of life of version 3.0.x.
</p>
<p>It should work on Linux (Fedora 4 or equivalent and newer distribs), MacOS 10.4 or newer, and Windows XP.
</p>
<p>Amongst the most noticeable changes, we can cite
<li>A fMRI module for BrainVISA, partly using Matlab and SPM, on the Linux version only at the moment</li>
<li>A new and faster database system in BrainVisa, which will need a conversion of older databases</li>
<li>the AimsAlgo part becomes open source (GPL/CeCILL license)</li>
<li>A volume rendering module in Anatomist</li>
<li>...</li>
</p>

<a name="2006_05_05"></a>
<h4>May 05, 2006, package update: 3.0.2</h4>
<p>A bugfix update that fixes several problems, especially stability issues on Windows.
</p>
<p>The Mac version now runs on MacOS 10.4 (and not on 10.3 anymore).</p>
<p>Solaris and Irix versions are still not maintained.
</p>

<a name="2005_10_17"></a>
<h4>October 17, 2005, package update: 3.0.1</h4>
<p>A bugfix update that fixes an important bug in the diffusion/tracking algorithms,
  a number of instabilities (rare crashes) in Anatomist, and adds some "minor" improvements,
  like multiple matlab versions support in BrainVisa, some optimizations in Anatomist when
  many complex objects (graphs) are loaded...
</p>
<p>Solaris and Irix versions are still not maintained (the solaris problem might have been
  solved recently but we need more testing and repackaging).
</p>

<a name="2005_06_29"></a>
<h4>June 29, 2005, brand new release: version 3.0 is out</h4>
<p>Finally we managed to release the new version of all of our software. Every project
  within the package has now version 3.0 (for simplicity).
</p>
<p>This package is released on Linux, Mac OS X and Windows XP systems, and <b>not for Solaris
or Irix</b>. This limitation is due to technical problems on our side that may or may not be
solved one day. Sorry for this.
</p>
<p>See the <a href="doc/axon/en/help/readme.html">release notes</a> and
<a href="doc/cartointernet/cartointernet_man/en/html/index.html">docs</a> for an overview of new features and changes.
</p>

<a name="2004_12_02"></a>
<h4>Dec. 2, 2004, stable release update: 2.3.5</h4>
<p>Just after the last update release, we found some bugs in Anatomist display (volume fusions
  in sagittal slices), and in the Mac version of BrainVisa (and probably the Windows version too),
  so here is another fix for these problems.
</p>

<a name="2004_11_19"></a>
<h4>Nov. 19, 2004, stable release update: 2.3.4</h4>
<p>A bugfix update package (2.3.4) is available in the download section. It fixes some bugs
(especially on the Windows version), and includes minor improvements such as matlab support
on Windows, SPM2 normalization matrixes importation, and a better installation script.
The package should work now when installed in a directory containing space characters.
</p>

<a name="2004_09_28"></a>
<h4>Sep. 28, 2004, MacOS X fix update: 2.3.3</h4>
<p>Well, the Mac version has not been maintained very regularly, and I have just noticed that the
2.3.2 binary version has been all messed-up, the distribution is incomplete and out of order.
I am sorry about that (but nobody has complained!), the fact is that I didn't have a Mac machine
to work on regularly. I have one now (thanks to Jean Rï¿½gis, La Timone).
</p>
<p>There is now a new binary package just for Mac, which runs on MacOS 10.3 and without the
need of a X11 server, and compiled with optimization on. Be careful, there are still a few
problems however:
  <li>Brainvisa run from the graphical interface of the Mac seems to frequently (and randomly)
  hang when running commands, so for this version at least, avoid running it by clicking on an
  icon, but use a terminal... We will investigate this strange phenonemnon when we have a bit of
  time...
  </li>
  <li>This package may not work on MacOS 10.2 and earlier. I have not tried myself, but...
  </li>
</p>

<h4>Jul. 8, 2004, stable release update: 2.3.2</h4>
Finally we have released a new package (2.3.2) which fixes various bugs encountered
in the 2.3 release. Amongst other fixes, we can cite:
<li>fix in BrainVisa database hierarchy description which could cause an ambiguity
  in the anatomical pipeline
</li>
<li>Fixes in filenames handling when filenames contain space charachers (which often
  happens on Windows)
</li>
<li>etc. See individual changelogs accessible via the
  <a href="doc/cartointernet/cartointernet_man/en/html/index.html">help pages</a> for more details
</li>
We do not plan a new version before the end of 2004 because many changes have been
started in both BrainVisa and Anatomist and we need time to finish, stablilize and
test all the new features.
<br>

<h4>Jan. 14, 2004, web server hosting change</h4>
Our website has moved to another place. It is still accessible on its "official" name
<a href="http://brainvisa.info">http://brainvisa.info</a>, but as it used to be just a
redirection, your browser has probably bookmarked it as http://brainvisa.free.fr. So
please update your bookmarks, the old page will be removed in a short time.<br>
The new server should be much faster and more reliable, and will allow us to set up
a bug tracking tool and a forum and other tools in the future.
<br>

<h4>Jan. 6, 2004, MacOS X fix update: 2.3.1</h4>
This is only a MacOS X-specific installation fix: it should overcome the "little
squares" syndrom on Anatomist and BrainVisa which do not properly display text
on some systems. Basically, I just upgraded some libraries (especially Qt) from the
Fink project.<br>
<b>Jan. 14:</b> Well, no in fact, it doesn't seem to help on MacOS 10.3 - use the trick in the
<a href="faq.html#install-bin-fonts">FAQ</a> to get non-antialiased fonts in Qt.
<br>

<h4>Dec. 18, 2003, new stable release: 2.3.0</h4>
Featuring BrainVISA 1.6, Anatomist 1.30, Aims 2.13, Vip 2.5 etc.<br>
At last we are ready to distribute a new version of BrainVISA, Anatomist and all the
other tools. Amongst other improvements, we can cite:
<li>in BrainVISA:
  <ul>
  <li>easier database setup which can now be done via the menus</li>
  <li>some improvements in the user interaction and viewers</li>
  <li>mproved (althrough still not complete) help system</li>
  <li>working diffusion / fiber tracking pipeline</li>
  </ul>
</li>
<li>In Anatomist:
  <ul>
  <li>minor GUI improvements: viewing images in radio or neuro convention,
    new setup options, visibility or usability comfort improvements</li>
  <li>new functionalities in the ROI drawing module (morphological math operations...)
  </li>
  <li>fixes and improvements in several volume formats IO...</li>
  </ul>
</li>
<li>Many other things which we did not keep track of. A bit more details are available
in the different projects changelogs, accessible via the new
<a href="doc/cartointernet/cartointernet_man/en/html/index.html">documentation and help pages</a></li>
<li>And maybe most of all, this is the first stable release to include a Windows version.
<br>
The Windows version is working and <em>nearly</em> fully functional, but there are
still some problems in BrainVISA cleanup when exiting, and VIDA and ECAT volume
formats are not supported. The other features seem to work well and processings produce
the same results as the Unix versions.<br>
The cache problem of the test releases for Windows is fixed, but at the cost of being
slower (possibly MUCH slower for large databases) because BrainVisa must systematically
scan every directory when accessing the database.</li>

<h4>Nov. 16, 2003, one more test package for Windows</h4>
<li>this pack doesn't use any unix command anymore</li>
<li>communication failures between BrainVisa and Anatomist have been fixed (I hope!),
after a long and hard fight</li>
<li>fixes little things like installation in path containing space characters,
ambiguous files naming on case-insensitive filesystems, ...</li>
<li>C and C++ sources have been compiled with optimization flags so it may be faster</li>

This is still definitely not the final version: there are still problems going on.
<li>I have experienced cache update problems with BrainVisa (the cache doesn't update
automatically, I have to make a "clearCache" and "updateCache" to make new files
visible in the database). We have understood what is going on: Fat32 filesystems don't
update directories modification date/time when a new file or directory is created
inside it. There should be no problem on NTFS filesystems and on Unix Samba-mounted
network drives. We will try to find a workarouond because it is very ennoying,
especially when importing a new subject MRI.</li>
<li>BrainVisa still doesn't exit cleanly and some temporary files may not be deleted
after it exits</li>
Oh, by the way, this package has been built on a linux filesystem, so sources (python
sources, C++ headers) are in unix ASCII convention. In the counterpart, files which
were symbolic links are OK on this version.

<h4>Nov. 04, 2003, another test package for Windows</h4>
This package fixes some problem with the previous one:
<li>some missing DLLs and paths in python prevented brainvisa from correctly
running commandlines (so almost nothing didn't work!)</li>
<li>a bunch of unix-only commands (like rm, cp, mv, touch...) have been
removed, but some are still around...</li>
<li>a better guess of the home directory is done so that <tt>.brainvisa</tt>
and <tt>.anatomist</tt> directories may be in a sane place even on other
windows than XP</li>

<h4>Nov. 02, 2003, first development package for Windows</h4>
There are still some problems (Brainvisa exits uncleanly and leaves some temporary
files, communications with Anatomist is sometimes lost...) but the main features
are working: BrainVisa, Anatomist and the image processing tools are there.<br>
Some volume IO formats are not supported at the moment: vida and ecat formats are not
compiled in the package. These formats require some libraries I don't have on
Windows (rpc library).<br>
But this is one of the last main steps towards the universal portability of the
platform...<br>
This test release is meant essentially for ourselves for debugging purposes, not for
end users yet. A new version is planned soon for all platforms (this month if we can
take the time to do it).<br>
Technically, I used the gcc compiler from the <a href="http://www.mingw.org">MinGW
environment</a>, and our configuration tools (build-config/configure/maker) in an
unix-like environment (<a href="http://www.mingw.org/msys.shtml">Msys</a> bash shell
coming with MinGW).<br>
Compiling with the gcc compiler from the <a href="http://www.cygwin.com/">Cygwin
distribution</a> is also possible (and certainly easier in fact), and would allow
to build vida and ecat format support because cygwin includes the missing rpc library.
But for licensing reasons, we cannot use cygwin: codes compiled with cygwin link
against the cygwin DLL which is GPL'd and must be used only for GPL'd code (which is not
the case of our algorithms).<br>
Building with Microsoft C++ compilers (Visual Studio .net) was not possible, the
compiler fails on some heavily templated C++ code: don't try the adventure, it's
useless.<br>
The binary distribution contains a copy of the commercial version of
<a href="http://www.trolltech.com">Qt</a> library DLL, and of the commercial version of
<a href="http://www.riverbankcomputing.co.uk">PyQt</a> for Windows.

<h4>May 23, 2003, stable version update: 2.2.3</h4>
Various little fixes (which may be important in some specific cases) in the
programs and the package installers, amongst which:
<li>Anatomist: fixes in buckets 3D renderings</li>
<li>Brainvisa: some problems with parameters links have been fixed</li>
<li>MacOS X installer: we used a tar program which was incompatible with
Apple's tar, it's fixed now</li>
<li>Linux/RedHat9 installer: we switch to the older threading system because
the new one causes problems with Python threads</li>
<li>Fixes in some lower-level commands: AimsClusterArg, ...</li>

<h4>Apr. 29, 2003, stable version update: 2.2.2</h4>
A few little fixes (mainly for linux):
<li>Anatomist: fixed a crash that could occur while in ROI edition and playing
    with several volumes with palette windows open</li>
<li>Anatomist: fixed the color change of some widgets which does not work with
    some KDE3 styles (this fix disapeared by mistake in the last stable
    anatomist release)</li>
<li>Anatomist: menu options to save the texture of some textured objects</li>
<li>We include again libcrypto and libssl in the linux package since they are
    required for some python modules</li>

<h4>Apr. 15, 2003, stable version update: 2.2.1</h4>
This new distribution fixes some installation problems (and offers more
precise installation instructions), and fixes a few BrainVisa bugs (the
help processes, diffusion package...).

<h4>Apr. 07, 2003, new stable release: 2.2</h4>
A new version of all software has been released, version 2.2 of the pack.
Binary packages for Linux (RedHat 7.3 and compatible distribs), Solaris, Irix
and MacOS X have been uploaded to the ftp site. See the downloads.
We changed the installation procedure: see the
.README file with each package. There is now only one file to get, the installer
is in it, but you have to unpack it yourself before running the install script.<br>
It features Anatomist 1.29, Brainvisa 1.5, Aims 2.12, Vip 2.4...<br>
<b>Main changes:</b> bugfixes (mainly in SPM format IO), many changes in
BrainVISA, shfj library is now renamed cartobase

<h4>Feb. 28, 2003, another MacOS X update</h4>
Other little fixes. You may still need to setup the default Qt font
using qtconfig. See the <a href="faq.html#inst-bin-fonts">FAQ</a> for details

<h4>Feb. 25, 2003: first MacOS X release (development)</h4>
A first development version for Mac/darwin compiled for X11 server. I hope
everything is in the package... It has not been thoroughtly tested yet...

<h4>Nov. 08, 2002: new stable release 2.1</h4>
This release is a version upgrade for <b>ALL</b> software: BrainVISA 1.4, Anatomist 1.28, etc.<br>
Amongst the most important changes:
<li>Introduction of functional preprocessing using SPM and Matlab in BrainVISA. This will evolve and more support for higher-level functional processing will be added in futire releases. You must have Matlab and SPM installed to use them.</li>
<li>If you wish to build from sources, the gcc-3.x compilers can now be used to
build all our C++ code.</li>
<b>Binary package notes:</b>
<li>This release is the first stable release to provide a binary package for
Irix</li>
<li>On Linux, we reverted from the behaviour of 2.02-2.04 distribs and we
systematically install Qt library again, because there may be system libraries
incompatibilities (C++ library), for example on RedHat 8 or Mandrake 9 systems using gcc-3.2. So <b>DON'T USE THE SHFJEnvironmentVariables.sh/.csh scripts in
your .cshrc/.bash_profile config scripts !</b> (or check they are compatible with your system first) - <a href="faq.html">see the FAQ</a> for more
details.</li>

<h4>Sep. 24, 2002: new stable 2.04 release for linux and SuSE-specific development release</h4>
(Installation fix release)
<li>2.04 stable release fixes an installation problem again: home-compiled Qt with good Jpeg support</li>
<li>SuSE-8.0 main (devel) release has been made because of system libraries incompatibilities with RedHat</li>
<br>
Changes between 2.04 and 2.03: Ooops, our Qt lib didn't support jpeg (!)<br>
Changes between 2.03 and 2.02: installation fix: provide a home-compiled Qt
library instead of RedHat's customized one, and install it only if the
target system doesn't already have it<br>

<h4>Aug. 22, 2002: first complete binary package for Irix</h4>
An Irix package is now available (development version) and contains the full
set of programs and libraries: brainvisa, anatomist and all tools<br>

<h4>09/08/2002: new stable release 2.02</h4>
Featuring Anatomist 1.27, BrainVISA 1.3 etc.<br>
Changes between 2.02 and 2.01: installation bug fixes<br>
Changes between 2.01 and 2.0: fixed a few broken functionalities in Anatomist 1.27 and some low-level Aims commands<br>

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BrainVisa now normally runs inside a virtual machine or a virtual container. It does not change "much" on how to use it, but there are a few things to know about it, and this situation also needs a few special configuration considerations.

BrainVisa now normally runs inside a virtual machine or a virtual container. It does not change “much” on how to use it, but there are a few things to know about it, and this situation also needs a few special configuration considerations.

A container has its own system, and its own users. But it's possible to use the same user identifier as on the host system. In BrainVISA containers, the ``bv`` command reuses the calling user identifier. But for several reasons we chose to use a separate home directory. In summary it's the same user, but a different home directory and different configuration files.

A container has its own system, and its own users. But it’s possible to use the same user identifier as on the host system. In BrainVISA containers, the 

 command reuses the calling user identifier. But for several reasons we chose to use a separate home directory. In summary it’s the same user, but a different home directory and different configuration files.

The user can use the host system data and files, and write data with the same access rights and identifier

Configuration files (like Unix ``.bash_profile`` and ``.bashrc`` files) are not shared, because they may contain items specific to the host sytem which would produce confusion, like ``PATH`` pointing to incompatible programs.

 files) are not shared, because they may contain items specific to the host sytem which would produce confusion, like 

Some of the account configuration would benefit from being shared, but thus is not. For instance ``ssh`` configuration and personal keys are not shared by default. See :ref:`ssh_keys_sing`.

Some of the account configuration would benefit from being shared, but thus is not. For instance 

 configuration and personal keys are not shared by default. See 

The container is a virtually separate machine from the host system. It does not see the same files and directories tree as the host system. In order to allow access to files (especially data to be processed) on the host filesystems, the container should be configured to mount the wanted directories.

The ``bv`` program invoked without arguments will start a configuration user interface which allows to add mount points to the BrainVisa installation.

 program invoked without arguments will start a configuration user interface which allows to add mount points to the BrainVisa installation.

SSH configuration is stored on Unix systems in a directory ``$HOME/.ssh``. This directory the the files there have restricted access permissions in order to ensure the confidentiality and security of the connections. It is not recommended, in a general way, to copy the private keys there to another location, even the container local home directory. Symbolic links are rejected by ssh for security reasons.

. This directory the the files there have restricted access permissions in order to ensure the confidentiality and security of the connections. It is not recommended, in a general way, to copy the private keys there to another location, even the container local home directory. Symbolic links are rejected by ssh for security reasons.

The solution is to use a ssh agent. The agent is not persistent, it has to be started on the host system by some mechanism (session manager, bash_profile...). We use ``keychain`` (``sudo apt-get install keychain``), which starts the agent for you and is able to reuse it in all sessions. We have something along these lines in ``~/.profile``::

The solution is to use a ssh agent. The agent is not persistent, it has to be started on the host system by some mechanism (session manager, bash_profile…). We use 

), which starts the agent for you and is able to reuse it in all sessions. We have something along these lines in 

The needed socket and environment variable pointing to it (``$SSH_AUTH_SOCK``) will be automatically mounted and setup by the ``bv`` command.

Matlab is generally installed on the host system and not in a container. In many laboratories Matlab is installed using a network install, and a license manager server. If Matlab has been installed for Linux in such a network, it is still possible to use it from the container.

mount/copy the licence file and/or set the ``MLM_LICENSE_FILE`` and ``LM_LICENSE_FILE`` environment variables.

Alternately, the user may just make the ``.matlab`` config files appear in the local container home directory. From the container shell, do::

  mkdir ~/.matlab
  cd ~/.matlab
  ln -s $CASA_HOST_HOME/.matlab/R*_licenses/ .

 config files appear in the local container home directory. From the container shell, do:

mkdir ~/.matlab
cd ~/.matlab
ln -s $CASA_HOST_HOME/.matlab/R*_licenses/ .

The BrainVISA framework is able to use several external neuroimaging software. Such software can be used from the container system, as soon as they have been installed for a compatible architecture (Linux) and can be run from a "normal" system of the same type as the container (Ubuntu 18.04 for this release), and they paths have been configured in BrainVISA, just like we did in former BrainVISA versions nor running in containers.

The BrainVISA framework is able to use several external neuroimaging software. Such software can be used from the container system, as soon as they have been installed for a compatible architecture (Linux) and can be run from a “normal” system of the same type as the container (Ubuntu 18.04 for this release), and they paths have been configured in BrainVISA, just like we did in former BrainVISA versions nor running in containers.

Namely, SPM (either standalone or using Matlab :ref:`when it is configured <Matlab>`), FSL, Freesurfer and other software can be used normally.

Brainvisa is using :soma_workflow:`Soma-Workflow <index.html>` to perform distributed processing.

The documentation of Soma-Workflow contains a section explaining :soma_workflow:`how to use it in a container <install_config.html#containerized-soma-workflow>`, both to run the server and to run BrainVisa software inside containers in jobs.

The documentation of Soma-Workflow contains a section explaining 

, both to run the server and to run BrainVisa software inside containers in jobs.

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The Cortical Surface toolbox is developed by the `MeCA research group in Marseille <http://www.meca-brain.org>`_. `The toolbox has an official URL <http://www.meca-brain.org/softwares/>`_.

`The toolbox has an official URL <http://www.meca-brain.org/softwares/>`_

This is the :axon:`BrainVISA toolbox doc <en/processes/categories/cortical_surface/category_documentation.html>`:

Problems with "raw" directive path:
InputError: [Errno 2] No such file or directory: '../../share/doc/axon/en/processes/categories/cortical_surface/category_documentation.html'.

Problems with “raw” directive path:
InputError: [Errno 2] No such file or directory: ‘../../share/doc/axon/en/processes/categories/cortical_surface/category_documentation.html’.

.. raw:: html
    :file: ../../../share/doc/axon/en/processes/categories/cortical_surface/category_documentation.html

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            <source src="https://brainvisa.info/doc/constellation/video/connectivity_profiles.mp4" />
          </video>
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          <img align="center" src="_static/images/constellation/B1_external_left.jpg" />
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            <source src="https://brainvisa.info/doc/constellation/video/small_brains.mp4" />
          </video>
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          <img align="center" src="_static/images/constellation/p1_fibres.jpg" />
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          <img align="center" src="_static/images/constellation/p2_fibres.jpg" />
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          <img align="center" src="_static/images/constellation/p3_fibres.jpg" />
      </div>
          <img align="center" src="_static/images/constellation/small_brains.jpg" />
      </div>

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older :    <!--#include file="carousels/car_constellation_big.html" -->

Cortex parcellation based on structural connectivity information. It performs group-wise parcellations, either on a "group-only" basis (one group result), or provides individual results, from a group analysis. The whole cortex is parcelled by patches.

Cortex parcellation based on structural connectivity information. It performs group-wise parcellations, either on a “group-only” basis (one group result), or provides individual results, from a group analysis. The whole cortex is parcelled by patches.

This toolbox, developed in NeuroSpin / UNATI lab, will be released "soon" when it is completely ready.

This toolbox, developed in NeuroSpin / UNATI lab, will be released “soon” when it is completely ready.

:morphoproc:`Constellation toolbox brainvisa help pages <categories/constellation/category_documentation.html>`

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Diffusion imaging processing, tractography and bundles analysis.

Connectomist-2 is developed by The UNIRS lab of NeuroSpin (Cyril Poupon), in a different software framework, but is also using Anatomist for all visualization needs. It features dMRI preprocessings (outliers detection, distortion correction), local diffusion models processing, tractography, and fibers bundles post-processing (bundles measurements, clustering...).

Connectomist-2 is developed by The UNIRS lab of NeuroSpin (Cyril Poupon), in a different software framework, but is also using Anatomist for all visualization needs. It features dMRI preprocessings (outliers detection, distortion correction), local diffusion models processing, tractography, and fibers bundles post-processing (bundles measurements, clustering…).

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Diffeomorphic structural-based cortical registration: 3D registration using sulcal constraints.

:morphoproc:`DISCO toolbox brainvisa help pages <categories/disco/category_documentation.html>`

.. |cati_logo| image:: images/labs/cati_logo.png
    :target: https://cati-neuroimaging.com
    :height: 32

image:: images/labs/cati_logo.png

.. |hbp_logo| image:: images/labs/hbp_logo.png
    :target: https://www.humanbrainproject.eu/

image:: images/labs/hbp_logo.png

DISCO is developed both by the `MeCA research group in Marseille <https://www.meca-brain.org/softwares/>`_, the |hbp_logo| `Human Brain Project <https://www.humanbrainproject.eu/>`_ and the |cati_logo| `CATI project labs <https://cati-neuroimaging.com>`_

`MeCA research group in Marseille <https://www.meca-brain.org/softwares/>`_

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A toolbox for BrainVISA developed by the |cati_logo| `CATI project labs <https://cati-neuroimaging.com>`_

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Semi-automatic segmentation toolbox for T2-weighted neonatal MRI images. This toolbox has been developed in Neurospin in the Developing Brain team. It is derived from :doc:`morphologist` with adaptations to take into account the T2-weighted image contrast, the partially myelinated nature of baby brains, thus involving some steps of manual corrections, alterning automatic and interactive parts.

Semi-automatic segmentation toolbox for T2-weighted neonatal MRI images. This toolbox has been developed in Neurospin in the Developing Brain team. It is derived from 

 with adaptations to take into account the T2-weighted image contrast, the partially myelinated nature of baby brains, thus involving some steps of manual corrections, alterning automatic and interactive parts.

The toolbox is used internally and has no public release up to now.

.. image:: images/logo_SACHA_white.jpg
    :target: http://www.aramislab.fr/software-2/
    :class: imgbox
    :width: 400

Automatic segmentation of hippocampus and amygdalia. Developed by the `Aramis team, ICM, Paris <http://www.aramislab.fr/>`_.

Automatic segmentation of hippocampus and amygdalia. Developed by the 

<div class="imgbox" style="width: 400px; height: 200px; line-height: 200px;">
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  </a>
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Developed by the `Aramis team, ICM, Paris <http://www.aramislab.fr/>`_.

BrainVISA toolboxes also include their own documentation embedded in BrainVISA user interface: toolboxes and processes docs are in in the main window right panel.
For instance:

* :morphoproc:`Morphologist <categories/morphologist/category_documentation.html>`
* :morphoproc:`Cortical surface <categories/cortical_surface/category_documentation.html>`
* :morphoproc:`FreeSurfer / Morphologist links <categories/freesurfer/category_documentation.html>`
* :morphoproc:`BrainRat <categories/brainrat/category_documentation.html>`
* :morphoproc:`Data management toolbox <categories/data management/category_documentation.html>`
* :morphoproc:`Future Constellation <categories/constellation/category_documentation.html>`
* :morphoproc:`Future DISCO <categories/disco/category_documentation.html>`

:morphoproc:`FreeSurfer / Morphologist links <categories/freesurfer/category_documentation.html>`

:morphoproc:`Data management toolbox <categories/data management/category_documentation.html>`

:morphoproc:`Future DISCO <categories/disco/category_documentation.html>`

:aimsdata:`AIMS <user_doc/index.html>` image processsing tools

:all_doc:`global index of all documentation provided on this website <doc_index.html>`

:all_doc:`global index of all commandlines help <index_commands.html>`

If you already know how to install, use this. Otherwise go to the explanations next.

BrainVISA is composed of a set of software, freely distributed in software bundles. Starting from **BrainVISA 5.0**, the software is distributed using virtualization. It means that there is only one BrainVISA version running on Linux but, thanks to virtualization, it can be used on any system. There are BrainVISA images for two free and open source virtualization technologies :

BrainVISA is composed of a set of software, freely distributed in software bundles. Starting from 

, the software is distributed using virtualization. It means that there is only one BrainVISA version running on Linux but, thanks to virtualization, it can be used on any system. There are BrainVISA images for two free and open source virtualization technologies :

`apptainer <https://apptainer.org/>`_: an operating-system-level virtualization (also known as containerization) technology well suited for high performance computing and for users without administration privileges (as compared to Docker, a more popular containerization technology).

: an operating-system-level virtualization (also known as containerization) technology well suited for high performance computing and for users without administration privileges (as compared to Docker, a more popular containerization technology).

`VirtualBox <https://www.virtualbox.org/>`_: an hypervisor allowing to run virtual machines and available on main operating systems (Linux, Windows, MacOs).

: an hypervisor allowing to run virtual machines and available on main operating systems (Linux, Windows, MacOs).

For Mac Silicon users, see the dedicated section :ref:`mac_silicon_install`.

Using virtualization allows to solve many porting and compatibility issues (especially packaging and distributing packages for many different operating systems). Now we only provide Linux containers for a single Linux system / version, which can be run on almost every host system.

modularity is gone: virtual images are not designed to be modular, so we cannot install just parts of it. You get the whole BrainVISA distribution. But in practice we never heard about anyone installing just a part of the packages in the previous distrubtions.

Programs must always be run through the virtualization layer, and not natively on the system. It can add some overhead, but this is light in most cases.

3D with hardware acceleration may not work out of the box. But it will, in most cases.

To use BrainVISA on your system, first read the :ref:`prerequisites` section. Then, if you just want to use the software, go to :ref:`apptainer_install` or :ref:`vbox_install` section. But if you want to develop BrainVISA related software, go to the :ref:`developers_install` section.

 section. But if you want to develop BrainVISA related software, go to the 

Prerequisite are the software that need to be installed on your computer in order to be able to install and use BrainVISA. They differ according to the virtualization technology you want to use (Apptainer or VirtualBox). We recommend using Apptainer for Linux and VirtualBox for Windows and MacOS. It works well but is more complex to setup (explaination below). Note that we had mitigate experiences on MacOS using both VirtualBox or Apptainer, even if both somewhat worked.

For Linux, two software must be installed : Python (version >= 3 is required for releases >= 5.1) and Apptainer (the successor of Singularity).
Most popular Linux distro come with Python already installed but if not, there are system package to install it. The name of the package to install is **python**. For example for Debian based distro::

Most popular Linux distro come with Python already installed but if not, there are system package to install it. The name of the package to install is 

Apptainer is now available as system package for popular Linux distributions.

If no package can be found for your system, then follow `Apptainer installation instructions <https://apptainer.org/docs/user/latest/quick_start.html#installation>`_

`Apptainer installation instructions <https://apptainer.org/docs/user/latest/quick_start.html#installation>`_

A recent version of `VirtualBox <https://www.virtualbox.org/>`_ ( >= 6.1) must be installed for the user of the system.

See the :casadistro:`troubleshooting section <technical.html#troubleshooting>`, especially :casadistro:`for Mac <technical.html#mac-vbox-troubleshooting>`. On Mac see also :ref:`mac_silicon_install`.

Using Apptainer on Windows works only with Windows 10 and requires a recent technology (deployed in late summer 2020, your system must have been updated afterward) allowing to run Linux in Windows. This technology, called Windows Subsystem For Linux 2 (WSL2) must be enabled on the system. Then a Linux distro must be installed from the Microsoft Store. Finally an X Windows server must be installed and started.

Once these steps are done, you will have a fully functionnal Linux running as a Windows 10 App. Therefore, you will have to follow the :ref:`linux_apptainer_prerequisites` section and then the :ref:`apptainer_install` section.

Once these steps are done, you will have a fully functionnal Linux running as a Windows 10 App. Therefore, you will have to follow the 

We recommend that you install Ubuntu 20.04. Follow the installation steps defined in `Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.

We recommend that you install Ubuntu 20.04. Follow the installation steps defined in 

`Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_

Linux is an old system with many programs using text-based user interface an no `graphical user interface (GUI) <https://en.wikipedia.org/wiki/Graphical_user_interface>`_. For now, it is necessary to install a third-party App to run any Linux App with a GUI, but Microsoft announced on //build 2020 that they will release soon an improvement that will not require any third-party component to run Linux GUI Apps on Windows Desktop (`source <https://techcommunity.microsoft.com/t5/windows-dev-appconsult/running-wsl-gui-apps-on-windows-10/ba-p/1493242>`_). The graphical interface for Linux is based on a technology called *X Windows* and the App to install is an *X Windows server*.

Linux is an old system with many programs using text-based user interface an no 

`graphical user interface (GUI) <https://en.wikipedia.org/wiki/Graphical_user_interface>`_

. For now, it is necessary to install a third-party App to run any Linux App with a GUI, but Microsoft announced on //build 2020 that they will release soon an improvement that will not require any third-party component to run Linux GUI Apps on Windows Desktop (

). The graphical interface for Linux is based on a technology called 

There exists many X Windows servers for Windows. For a free and open source one, we recommend `VcXsrv <https://sourceforge.net/projects/vcxsrv/>`_. On its web page, click on the *Download* button to get an installer program. Once installed, you can run *X Launch* to configure and start the server. The following images shows the options we recommend for the various steps of the setup. On the last step, you can save the configuration in a file that will allow to quickly restart the server by just double clicking on the saved file.

There exists many X Windows servers for Windows. For a free and open source one, we recommend 

 button to get an installer program. Once installed, you can run 

 to configure and start the server. The following images shows the options we recommend for the various steps of the setup. On the last step, you can save the configuration in a file that will allow to quickly restart the server by just double clicking on the saved file.

On Mac XQuartz is part of the system but needs some setup: :casadistro:`see also this doc <technical.html#gui-is-not-working-in-singularity>`.

Create an installation directory::

  mkdir $HOME/brainvisa-5.0.0

Download the BrainVISA image found below into this new directory. It's a ``.sif`` file, for instance ``brainvisa-5.0.0.sif``.

Download the BrainVISA image found below into this new directory. It’s a 

Run Apptainer using this image, with an option to tell it to run its setup procedure. The installation directory should be passed::

  apptainer run -c -B $HOME/brainvisa-5.0.0:/casa/setup $HOME/brainvisa-5.0.0/brainvisa-5.0.0.sif

(note the option ``-c`` option which avoids mixing up user configuration files from the host in the container)

Run Apptainer using this image, with an option to tell it to run its setup procedure. The installation directory should be passed:

apptainer run -c -B $HOME/brainvisa-5.0.0:/casa/setup $HOME/brainvisa-5.0.0/brainvisa-5.0.0.sif

 option which avoids mixing up user configuration files from the host in the container)

set the ``bin/`` directory of the installation directory in the ``PATH`` environment variable of your host system config, typically in ``$HOME/.bashrc`` or ``$HOME/.bash_profile`` if you are using a Unix Bash shell::

  export PATH="$HOME/brainvisa-5.0.0/bin:$PATH"

Optionally, you may want to run the configuration GUI, through the ``bv`` program. Since BrainVISA is running in a container, it cannot access your computer directories unless you make them available to the container. Adding directories is done graphically, simply using the following command::

  bv

Optionally, you may want to run the configuration GUI, through the 

 program. Since BrainVISA is running in a container, it cannot access your computer directories unless you make them available to the container. Adding directories is done graphically, simply using the following command:

Installation is finished, you can run programs from the container.

There are several ways actually:

#. The simplest way, call commands directly from the above ``PATH`` like if they were on the host machine::

      # run programs
      AimsFileInfo --info
      anatomist
      brainvisa

2. Using :casadistro:`bv <bv_command.html>` interface to containers or :casadistro:`casa_distro <casa_distro_command.html>`:

  The :casadistro:`bv <bv_command.html>` program is found in each :casadistro:`install directory <concepts.html#environment>` into ``bin`` subdirectory in order to be always compatible with this installed environment (thus you can install and use several BrainVISA version at the same time).

  * :casadistro:`bv <bv_command.html>` accepts an executable program name as sub-command, it allows to run programs installed inside the container, for instance::

        bv brainvisa
        bv anatomist
        bv AimsFileInfo -h

    or to open an interactive shell in the container::

        bv bash

    More options may be used. :casadistro:`See the complete documentation of the bv command <bv_command.html>`.

The simplest way, call commands directly from the above ``PATH`` like if they were on the host machine::

   # run programs
   AimsFileInfo --info
   anatomist
   brainvisa

Using :casadistro:`bv <bv_command.html>` interface to containers or :casadistro:`casa_distro <casa_distro_command.html>`:

The :casadistro:`bv <bv_command.html>` program is found in each :casadistro:`install directory <concepts.html#environment>` into ``bin`` subdirectory in order to be always compatible with this installed environment (thus you can install and use several BrainVISA version at the same time).

* :casadistro:`bv <bv_command.html>` accepts an executable program name as sub-command, it allows to run programs installed inside the container, for instance::

      bv brainvisa
      bv anatomist
      bv AimsFileInfo -h

  or to open an interactive shell in the container::

      bv bash

  More options may be used. :casadistro:`See the complete documentation of the bv command <bv_command.html>`.

 subdirectory in order to be always compatible with this installed environment (thus you can install and use several BrainVISA version at the same time).

:casadistro:`bv <bv_command.html>` accepts an executable program name as sub-command, it allows to run programs installed inside the container, for instance::

    bv brainvisa
    bv anatomist
    bv AimsFileInfo -h

or to open an interactive shell in the container::

    bv bash

More options may be used. :casadistro:`See the complete documentation of the bv command <bv_command.html>`.

 accepts an executable program name as sub-command, it allows to run programs installed inside the container, for instance:

If you are using BrainVISA using Apptainer or Docker containers, graphical software need to run the containers with a graphical "bridge": a *X server* has to be running on the host system, and 3D display may or may not work. The options ``gui=yes`` and ``opengl`` of the :casadistro:`bv command <bv_command.html>` try to handle common cases, possibly using Nvidia proprietary OpenGL implementation and drivers from the host system.

Note that the option ``gui=yes`` is now the default, thus it is not needed.

If you are using BrainVISA using Apptainer or Docker containers, graphical software need to run the containers with a graphical “bridge”: a 

 has to be running on the host system, and 3D display may or may not work. The options 

 try to handle common cases, possibly using Nvidia proprietary OpenGL implementation and drivers from the host system.

see the :casadistro:`troubleshooting <technical.html#troubleshooting>` section, especially the :casadistro:`OpenGL troubleshooting <technical.html#sing-opengl>`, :casadistro:`Singularity on Mac <technical.html#mac-sing-troubleshooting>` and :casadistro:`Singularity on Windows <technical.html#win-sing-troubleshooting>` subsections.

See also the :casadistro:`OpenGL troubleshooting <technical.html#opengl-troubleshooting>` section for if you experience problems using 3D rendering.

To use BrainVISA with **VirtualBox**, the procedure is roughly the same on Linux, Windows and Mac machines.

, the procedure is roughly the same on Linux, Windows and Mac machines.

`VirtualBox <https://www.virtualbox.org/>`_ must be installed for the user of the system.

Download a VirtualBox image foud in the following table.

**Note that you don't need to download an image built for your host system**, the virtualization allows precisely to run, for instance, an Ubuntu-18.04 image, on any host system (Linux, Windows, or Mac).

Available VirtualBox BrainVisa images:

  .. raw:: html

      <div id="brainvisa-vbox"></div>

**Note that you don't need to download an image built for your host system**

Note that you don’t need to download an image built for your host system

, the virtualization allows precisely to run, for instance, an Ubuntu-18.04 image, on any host system (Linux, Windows, or Mac).

in VirtualBox, import the downloaded image - some configuration (memory, CPU, video, sound etc) may be useful for it in VirtualBox.

some mount points to the host filesystem can be added to see the host filesystem directories from the VM.

in the running Linux virtual machine, BrainVISA is installed and configured.  You can open a terminal and type:

.. code-block:: bash

    AimsFileInfo -h
    brainvisa
    anatomist

The virtual machine has a configured user named "brainvisa", with the password "brainvisa", which has ``sudo`` (admin) permissions.

The virtual machine has a configured user named “brainvisa”, with the password “brainvisa”, which has 

see the :casadistro:`troubleshooting <technical.html#troubleshooting>` section, especially the :casadistro:`VirtualBox on Mac <technical.html#mac-vbox-troubleshooting>` subsection.

The :ref:`requirements <prerequisites>` are the same as for user installs. The main difference is that developers will get source code from source repositories, and compile the whole code. To do that, we have published "developer images" which contain all the required development tools and libraries. To date, we only support development environments using Apptainer. But we plan to provide image and instruction for VirtualBox too.

 are the same as for user installs. The main difference is that developers will get source code from source repositories, and compile the whole code. To do that, we have published “developer images” which contain all the required development tools and libraries. To date, we only support development environments using Apptainer. But we plan to provide image and instruction for VirtualBox too.

If you want to develop software using the BrainVISA environment, you are advised to read the :casadistro:`developer <developer.html>` section of the :casadistro:`Casa-Distro project <index.html>`.

If you want to develop software using the BrainVISA environment, you are advised to read the 

  mkdir -p $HOME/casa_distro/brainvisa-opensource-master

(note that we are using a slightly different directories organization from the user case, because the images here can be reused and shared betwen several development configurations - but this organization is not mandatory, it will just make things simpler for the management tool :casadistro:`casa_distro <index.html>` if it is used later)

(note that we are using a slightly different directories organization from the user case, because the images here can be reused and shared betwen several development configurations - but this organization is not mandatory, it will just make things simpler for the management tool 

Download the ``casa-dev`` image found here (https://brainvisa.info/download/), preferably into the ``$HOME/casa_distro`` directory. It's a ``.sif`` file, for instance ``casa-dev-5.0.sif``.

Execute the container image using Apptainer, with an option to tell it to run its setup procedure. The installation directory should be passed, and it will require additional parameters to specify the :casadistro:`development environment <concepts.html#environment>` characteristics. Namely a :casadistro:`distro <concepts.html#distro>` argument will tell which projects set the build will be based on (valid values are `opensource`, `brainvisa`, `cea` etc.), a :casadistro:`branch <concepts.html#branch>` argument will be `master`, `latest_release` etc., and other arguments are optional::

  apptainer run -c -B $HOME/casa_distro/brainvisa-opensource-master:/casa/setup $HOME/casa_distro/casa-dev-5.0.sif branch=master distro=opensource

Execute the container image using Apptainer, with an option to tell it to run its setup procedure. The installation directory should be passed, and it will require additional parameters to specify the 

 argument will tell which projects set the build will be based on (valid values are 

apptainer run -c -B $HOME/casa_distro/brainvisa-opensource-master:/casa/setup $HOME/casa_distro/casa-dev-5.0.sif branch=master distro=opensource

  export PATH="$HOME/casa_distro/brainvisa-opensource-master/bin:$PATH"

Optionally, you may want to run the configuration GUI, through the ``bv`` program: as programs are actually running in a container or a virtual machine (transparently), the user may have to configure additional mount points to actually see his data and working directories from his host machine in the container. This is done graphically, simply using::

  bv

 program: as programs are actually running in a container or a virtual machine (transparently), the user may have to configure additional mount points to actually see his data and working directories from his host machine in the container. This is done graphically, simply using:

The development system is ready in the container, and BrainVISA build system (:bv-cmake:`brainvisa-cmake <index.html>`) is available. You may need to configure the projects you want to retreive / build, and set the login / passwords in the sources repositories for non-public sources, if needed.

* You can open a terminal using::

    bv bash

  then build from within the terminal::

    bv_maker

* or start it from outside the container::

    bv_maker

  (this will run the :casadistro:`bv <bv_command.html>` program wich will call commands inside the container)

The development system is ready in the container, and BrainVISA build system (

) is available. You may need to configure the projects you want to retreive / build, and set the login / passwords in the sources repositories for non-public sources, if needed.

You can open a terminal using::

  bv bash

then build from within the terminal::

  bv_maker

or start it from outside the container::

  bv_maker

(this will run the :casadistro:`bv <bv_command.html>` program wich will call commands inside the container)

Technically, ``bv`` is a simplified version of :casadistro:`casa_distro <casa_distro_command.html>` which is contained inside a single *environment* (distribution installation) and only allows to run and configure this environment. See the doc of :casadistro:`casa-distro <index.html>` for more details.

 (distribution installation) and only allows to run and configure this environment. See the doc of 

import the image and configure it in VirtualBox :ref:`just like the BrainVisa users images <vbox_install>`

inside the image, edit, check or complete the config files, especially ``/casa/conf/svn.secret`` and ``/casa/conf/bv_maker.cfg``

inside the image, edit, check or complete the config files, especially 

the develper tools and directories are already setup. The ``bv_maker`` command is available.

Mac machines are now using ARM processors which architecture is not compatible with the x86_64 distribution that we provide. Even running a virtual machine is a challenge.

We have a recipe to make things together, which has been sent by an anonymous user, who we thank gratefully. This solution uses CPU emulation plus a virtual machine. Here are the instructions:

Download and convert vbox image to QEMU (the exact URL may change).

$ tar xvf brainvisa-5.1.2.ova
x brainvisa-5.1.2.ovf
x brainvisa-5.1.2-disk001.vmdk

This creates the 2 files shown above. The key file here is the VirtualBox disk image - the ``.vmdk`` file.

This creates the 2 files shown above. The key file here is the VirtualBox disk image - the 

Memory: leave this as default (4096 MB) for now - can increase this later if needed.

CPU: select 2 CPU cores for now - can increase this later. (NB: This VM seems to need >=2 cores, I found reasonable performance with 4 cores)

On Storage page: Select how much storage you need your virtual machine to have.

On Shared Directory page: Ignore for now and click ``Continue``. (See Step 5 to set up)

This will now open up the full VM settings, where you'll need to do the following:

This will now open up the full VM settings, where you’ll need to do the following:

System tab: Check ``Force Multicore``. (This seemed necessary to get this VM to work, not 100% sure why!)

. (This seemed necessary to get this VM to work, not 100% sure why!)

``Drives -> IDE Drive``: Click ``Delete`` to delete the virtual hard drive that UTM created for you.

``Drives -> New... -> Import...``: Navigate to the ``brainvisa-5.1.2-disk001.vmdk`` file extracted from the ``.ova`` file earlier.

Click ``Save``. It'll then take a few seconds to import the disk image and create your new VM.
Your new VM should hopefully then appear in the main UTM screen.

. It’ll then take a few seconds to import the disk image and create your new VM.

This should show a Linux bootup sequence, then a Linux desktop (running the LXDE desktop environment) after ~10 seconds.

If it seems to get stuck at "Set console scheme", make sure you picked at least 2 CPU cores & Force Multicore. You can change these via the VM settings.

If it seems to get stuck at “Set console scheme”, make sure you picked at least 2 CPU cores & Force Multicore. You can change these via the VM settings.

Once the VM is working, you can delete the downloaded ``.ova`` (and extracted ``.ovf`` & ``.vmdk`` files) - UTM will have made its own working copy of this. You can see where this is by right-clicking on the VM and picking ``"Show in Finder"`` from the menu.

 files) - UTM will have made its own working copy of this. You can see where this is by right-clicking on the VM and picking 

Configuring the Shared Directory: This follows steps outlined by UTM
(https://docs.getutm.app/guest-support/linux/#virtfs)

(

Close your Virtual machine, right click on the machine and select ``edit`` to open settings.

Close your Virtual machine, right click on the machine and select 

Go to ``Sharing``, change ``Directory Share Mode`` to VirtFS and select a folder path you which to share between host and virtual machines.

 to VirtFS and select a folder path you which to share between host and virtual machines.

Now start and open terminal within the virtual machine. Enter the following commands: ::

Now start and open terminal within the virtual machine. Enter the following commands:

$ sudo mkdir [mount point]
$ sudo mount -t 9p -o trans=virtio share [mount point] -oversion=9p2000.L

Where ``[mount point]`` is the desired destination path. For example: ``/media/share``
(NB: When running sudo, you be asked for the root password for brainvisa. The password is: ``brainvisa``)

(NB: When running sudo, you be asked for the root password for brainvisa. The password is: 

Your shared directory should now be visible under ``Devices``, you may need to restart your machine. From this volume you can drag and drop files directly into BrainVisa applications.

, you may need to restart your machine. From this volume you can drag and drop files directly into BrainVisa applications.

Three main programs, ``brainvisa``, ``anatomist``, and ``morphologist`` are available directly in the ``bin`` directory of the installed software. A lot of other programs are also present here.

 directory of the installed software. A lot of other programs are also present here.

:doc:`anatomist <anatomist>` is the interactive 3D visualization software.

:morphouiusr:`morphologist <index.html>` is the new user interface for the main :doc:`morphologist` pipeline.

``brainvisa`` is the user interface to :axonusr:`Axon <index.html>`, which will generally be the entry point to all other applications and toolboxes. You may also have access to ``morphologist`` and ``anatomist`` from the ``brainvisa`` program.

, which will generally be the entry point to all other applications and toolboxes. You may also have access to 

Once started, brainvisa will need a bit of configuration: go to the "BrainVISA / Preferences" menu, and setup especially paths to external software such as Matlab, SPM, FSL or Freesurfer if you have installed them.

Once started, brainvisa will need a bit of configuration: go to the “BrainVISA / Preferences” menu, and setup especially paths to external software such as Matlab, SPM, FSL or Freesurfer if you have installed them.

BrainVISA is working with files and directories organizations, and local databases, more generally regrouped under the term "databases". You will have to setup at least one to make it work in optimal conditions. At the beginning a database is a new, empty directory, where BrainVISA will import unprocessed data and write processed data.

BrainVISA is working with files and directories organizations, and local databases, more generally regrouped under the term “databases”. You will have to setup at least one to make it work in optimal conditions. At the beginning a database is a new, empty directory, where BrainVISA will import unprocessed data and write processed data.

Before running processing, raw data thus has to be imported in such a database: use the ":morphoproc:`Data management <categories/data management/category_documentation.html>`" tools, ":morphoproc:`import <categories/data management/import/category_documentation.html>`" to do so. For T1 MRI processing (using Morphologist), you will typically use the ":morphoproc:`Import T1 MRI <ImportT1MRI.html>`" process, or the ":morphoproc:`Import DICOM T1 MRI <ImportT1MRI_Dicom.html>`" process. Appropriate import processes are generally also found in processing toolboxes.

Before running processing, raw data thus has to be imported in such a database: use the “

” to do so. For T1 MRI processing (using Morphologist), you will typically use the “

” process. Appropriate import processes are generally also found in processing toolboxes.

.. image:: images/importt1.png
    :align: center
    :width: 600

More information may be found in the :axonusr:`Axon tutorial <tutorial.html>` and, more generally in the :axonusr:`Axon documentation <index.html>`.

As the whole set of software contains several sub-packages, each may have its specific licencing policy. See individual modules for licence information.

Some are "really" free and open source (`CeCILL-B <http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html>`_, BSD-like licence), some are `CeCILL-v2 <http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html>`_ (GPL-compatible), and some are closed source with free binary distribution for non-profit usage.

 (GPL-compatible), and some are closed source with free binary distribution for non-profit usage.

The core is *as free as possible*: CeCILL-B when possible, or CeCILL-v2 when using PyQt which is GPL:

: CeCILL-B when possible, or CeCILL-v2 when using PyQt which is GPL:

Anatomist is CeCILL-B, with some additional python plugins which are bound to GPL.

CeCILL licences are compatible with their GPL or BSD equivalent, but with additional legal precisions for french laws. See http://www.cecill.info/index.en.html

CeCILL licences are compatible with their GPL or BSD equivalent, but with additional legal precisions for french laws. See 

This basically leaves the possibility for toolboxes developers to choose the licence which suits them (open or closed), with some PyQt (GUI) parts which have to be GPL-compatible.

Morphologist, BrainRAT, cortical_surface and some other toolboxes also include closed-source code in their algorithmic parts. They can be used freely for non-profit usage.

* Typically academic research applications are OK.
* Commercial applications of these toolboxes should contact their authors before proceeding.

Commercial applications of these toolboxes should contact their authors before proceeding.

Versions 4.5-4.6:
:doc:`Download for older (4.6 and earlier) versions <download-4.6>`

Version 4.4 and older:
| binaries: https://brainvisa.info/download/vintage_versions/

Unknown target name: "https://apptainer.org/docs/admin/main/installation.html#installation-on-windows-or-mac".

Hyperlink target "linux-apptainer-prerequisites" is not referenced.

**Online and Offline installers**

You normally need the "online" installer variants, which are more lightweight: they will download packages which need to be installed, and only them, once they are selected. The "offline" installers contain all the builtin packages, and thus do not need to download them when installing. Use them to install BrainVISA on computers which cannot access the internet network. Most of the time we don't even build them because they are big. We make them when there is a need for them.

You normally need the “online” installer variants, which are more lightweight: they will download packages which need to be installed, and only them, once they are selected. The “offline” installers contain all the builtin packages, and thus do not need to download them when installing. Use them to install BrainVISA on computers which cannot access the internet network. Most of the time we don’t even build them because they are big. We make them when there is a need for them.

.. image:: images/cort_download.png
    :align: left
    :width: 96

<div class="download_4_6_1" id="download_4_6_1">
    <table border="1" class="docutils">
        <thead>
            <tr class="row-odd">
                <th class="head">OS</th>
                <th class="head">Online</th>
                <th class="head">Size</th>
                <th class="head">md5</th>
                <th class="head">Repository</th>
            </tr>
        </thead>
        <tbody>
        <tr>
          <td>Linux 64 bits (glibc 2.23) (built on Ubuntu 16.04)</td>
          <td><a href="../packages/4.6.1/linux64-glibc-2.23/brainvisa-installer/brainvisa_installer-4.6.1-linux64-glibc-2.23-online">Download (bin)</a></td>
          <td>23.0 MB</td>
          <td><a href="../packages/4.6.1/linux64-glibc-2.23/brainvisa-installer/brainvisa_installer-4.6.1-linux64-glibc-2.23-online.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.1/linux64-glibc-2.23/packages">https://brainvisa.info/packages/4.6.1/linux64-glibc-2.23/packages</a></td>
        </tr>
        <tr>
          <td>Linux 64 bits (glibc 2.15) (built on Ubuntu 12.04)</td>
          <td><a href="../packages/4.6.1/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.6.1-linux64-glibc-2.15-online">Download (bin)</a></td>
          <td><a href="../packages/4.6.1/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.6.1-linux64-glibc-2.15-online.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.1/linux64-glibc-2.15/packages">https://brainvisa.info/packages/4.6.1/linux64-glibc-2.15/packages</a></td>
        </tr>
        <tr>
          <td>Linux 64 bits (glibc 2.6) (built on Mandriva 2008)</td>
          <td><a href="../packages/4.6.1/linux64-glibc-2.6/brainvisa-installer/brainvisa_installer-4.6.1-linux64-glibc-2.6-online">Download (bin)</a></td>
          <td><a href="../packages/4.6.1/linux64-glibc-2.6/brainvisa-installer/brainvisa_installer-4.6.1-linux64-glibc-2.6-online.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.1/linux64-glibc-2.6/packages">https://brainvisa.info/packages/4.6.1/linux64-glibc-2.6/packages</a></td>
        </tr>
        <tr>
          <td>MacOS 32 bits (built on MacOS 10.5)</td>
          <td><a href="../packages/4.6.1/osx/brainvisa-installer/brainvisa_installer-4.6.1-osx-online.dmg">Download (bin)</a></td>
          <td>9.9 MB</td>
          <td><a href="../packages/4.6.1/osx/brainvisa-installer/brainvisa_installer-4.6.1-osx-online.dmg.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.1/osx/packages">https://brainvisa.info/packages/4.6.1/osx/packages</a></td>
        </tr>
        <tr>
          <td>Windows 32 bits (built on Windows 7)</td>
          <td><a href="../packages/4.6.1/win32/brainvisa-installer/brainvisa_installer-4.6.1-win32-online.exe">Download (bin)</a></td>
          <td>18.0 MB</td>
          <td><a href="../packages/4.6.1/win32/brainvisa-installer/brainvisa_installer-4.6.1-win32-online.exe.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.1/win32/packages">https://brainvisa.info/packages/4.6.1/linux64-win32/packages</a></td>
        </tr>
        <tr>
          <td>Windows 64 bits (built on Windows 7)</td>
          <td><a href="../packages/4.6.1/win64/brainvisa-installer/brainvisa_installer-4.6.1-win64-online.exe">Download (bin)</a></td>
          <td><a href="../packages/4.6.1/win64/brainvisa-installer/brainvisa_installer-4.6.1-win64-online.exe.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.1/win64/packages">https://brainvisa.info/packages/4.6.1/linux64-win64/packages</a></td>
        </tr>
        <tr>
          <td>OS-independent data (used by all installers)</td>
          <td>-</td><td>-</td><td>-</td>
          <td><a href="../download/packages/4.6.1/data/packages">https://brainvisa.info/packages/4.6.1/data/packages</a></td>
        </tr>
        </tbody>
    </table>
</div>

<div class="download_4_6_0" id="download_4_6_0">
        <thead>
            </tr>
        </thead>
        <tbody>
        <tr>
          <td><a href="../packages/4.6.0/linux64-glibc-2.23/brainvisa-installer/brainvisa_installer-4.6.0-linux64-glibc-2.23-online">Download (bin)</a></td>
          <td><a href="../packages/4.6.0/linux64-glibc-2.23/brainvisa-installer/brainvisa_installer-4.6.0-linux64-glibc-2.23-online.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.0/linux64-glibc-2.23/packages">https://brainvisa.info/packages/4.6.0/linux64-glibc-2.23/packages</a></td>
        </tr>
        <tr>
          <td><a href="../packages/4.6.0/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.6.0-linux64-glibc-2.15-online">Download (bin)</a></td>
          <td><a href="../packages/4.6.0/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.6.0-linux64-glibc-2.15-online.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.0/linux64-glibc-2.15/packages">https://brainvisa.info/packages/4.6.0/linux64-glibc-2.15/packages</a></td>
        </tr>
        <tr>
          <td><a href="../packages/4.6.0/linux64-glibc-2.6/brainvisa-installer/brainvisa_installer-4.6.0-linux64-glibc-2.6-online">Download (bin)</a></td>
          <td><a href="../packages/4.6.0/linux64-glibc-2.6/brainvisa-installer/brainvisa_installer-4.6.0-linux64-glibc-2.6-online.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.0/linux64-glibc-2.6/packages">https://brainvisa.info/packages/4.6.0/linux64-glibc-2.6/packages</a></td>
        </tr>
        <tr>
          <td><a href="../packages/4.6.0/osx/brainvisa-installer/brainvisa_installer-4.6.0-osx-online.dmg">Download (bin)</a></td>
          <td>10.0 MB</td>
          <td><a href="../packages/4.6.0/osx/brainvisa-installer/brainvisa_installer-4.6.0-osx-online.dmg.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.0/osx/packages">https://brainvisa.info/packages/4.6.0/osx/packages</a></td>
        </tr>
        <tr>
          <td><a href="../packages/4.6.0/win32/brainvisa-installer/brainvisa_installer-4.6.0-win32-online.exe">Download (bin)</a></td>
          <td><a href="../packages/4.6.0/win32/brainvisa-installer/brainvisa_installer-4.6.0-win32-online.exe.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.0/win32/packages">https://brainvisa.info/packages/4.6.0/linux64-win32/packages</a></td>
        </tr>
        <tr>
          <td><a href="../packages/4.6.0/win64/brainvisa-installer/brainvisa_installer-4.6.0-win64-online.exe">Download (bin)</a></td>
          <td><a href="../packages/4.6.0/win64/brainvisa-installer/brainvisa_installer-4.6.0-win64-online.exe.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.6.0/win64/packages">https://brainvisa.info/packages/4.6.0/linux64-win64/packages</a></td>
        </tr>
        <tr>
          <td><a href="../download/packages/4.6.0/data/packages">https://brainvisa.info/packages/4.6.0/data/packages</a></td>
        </tr>
        </tbody>
    </table>
</div>

<div class="download_4_5_0" id="download_4_5_0">
        <thead>
                <th class="head">Offline</th>
                <th class="head">Offline md5</th>
            </tr>
        </thead>
        <tbody>
        <tr>
          <td><a href="../packages/4.5.0/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.15-online">Download (bin)</a></td>
          <td>23.7 MB</td>
          <td><a href="../packages/4.5.0/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.15-online.md5">Download (txt)</a></td>
          <td><a href="../packages/4.5.0/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.15-offline">Download (bin)</a></td>
          <td>1.0 GB</td>
          <td><a href="../packages/4.5.0/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.15-offline.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.5.0/linux64-glibc-2.15/packages">https://brainvisa.info/packages/4.5.0/linux64-glibc-2.15/packages</a></td>
        </tr>
        <tr>
          <td><a href="../packages/4.5.0/linux64-glibc-2.6/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.6-online">Download (bin)</a></td>
          <td><a href="../packages/4.5.0/linux64-glibc-2.6/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.6-online.md5">Download (txt)</a></td>
          <td><a href="../packages/4.5.0/linux64-glibc-2.6/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.6-offline">Download (bin)</a></td>
          <td>1012 MB</td>
          <td><a href="../packages/4.5.0/linux64-glibc-2.6/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.6-offline.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.5.0/linux64-glibc-2.6/packages">https://brainvisa.info/packages/4.5.0/linux64-glibc-2.6/packages</a></td>
        </tr>
        <tr>
          <td>Linux 32 bits (glibc 2.3) (built on Fedora 4)</td>
          <td><a href="../packages/4.5.0/linux32-glibc-2.3/brainvisa-installer/brainvisa_installer-4.5.0-linux32-glibc-2.3-online">Download (bin)</a></td>
          <td>22.5 MB</td>
          <td><a href="../packages/4.5.0/linux32-glibc-2.3/brainvisa-installer/brainvisa_installer-4.5.0-linux32-glibc-2.3-online.md5">Download (txt)</a></td>
          <td>-</td>
          <td><a href="../download/packages/4.5.0/linux32-glibc-2.3/packages">https://brainvisa.info/packages/4.5.0/linux32-glibc-2.3/packages</a></td>
        </tr>
        <tr>
          <td><a href="../packages/4.5.0/osx/brainvisa-installer/brainvisa_installer-4.5.0-osx-online.dmg">Download (bin)</a></td>
          <td>9.4 MB</td>
          <td><a href="../packages/4.5.0/osx/brainvisa-installer/brainvisa_installer-4.5.0-osx-online.dmg.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.5.0/osx/packages">https://brainvisa.info/packages/4.5.0/osx/packages</a></td>
        </tr>
        <tr>
          <td><a href="../packages/4.5.0/win32/brainvisa-installer/brainvisa_installer-4.5.0-win32-online.exe">Download (bin)</a></td>
          <td>14.7 MB</td>
          <td><a href="../packages/4.5.0/win32/brainvisa-installer/brainvisa_installer-4.5.0-win32-online.exe.md5">Download (txt)</a></td>
          <td><a href="../download/packages/4.5.0/win32/packages">https://brainvisa.info/packages/4.5.0/win32/packages</a></td>
        </tr>
        <tr>
          <td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td>
          <td><a href="../download/packages/4.5.0/data/packages">https://brainvisa.info/packages/4.5.0/data/packages</a></td>
        </tr>
        </tbody>
    </table>
</div>

Download the installer program for your operating system. Choose the appropriate online / offline installer (`see above <#binaries>`_)

Download the installer program for your operating system. Choose the appropriate online / offline installer (

follow the instructions to select the desired packages to install

You will need a network connection during installation when using the "online" installers.

You will need a network connection during installation when using the “online” installers.

Three main programs, ``BrainVISA``, ``anatomist``, and ``morphologist`` are available directly in the root directory of the installed software.

 are available directly in the root directory of the installed software.

A lot of other programs are located in the ``bin`` subdirectory.

Note that packages repositories may be configured in the installation program, and additional repositories may be added, for instance to include packages maintained by external labs.

Once installed, the setup program ``BrainVISA_Suite-Update`` will allow to update some packages, install new ones, or to setup additional repositories.

 will allow to update some packages, install new ones, or to setup additional repositories.

It is also possible to use the **Linux version of BrainVISA on Windows 10** using the *Ubuntu Windows Subsystem for Linuw (WSL)*. Here are the instructions, as reported by one of our users (thanks François Tadel):

. Here are the instructions, as reported by one of our users (thanks François Tadel):

In Windows 10: Enable WSL and Ubuntu, there are many online tutorials available for that, for example: https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/

In Windows 10: Enable WSL and Ubuntu, there are many online tutorials available for that, for example: 

In Windows 10: Install the free version of MobaXterm:
https://mobaxterm.mobatek.net/

In MobaXterm: Menu ``Settings > Configuration > tab X11``:

 - Xorg version: **Cygwin_1.16.3**
 - OpenGL acceleration: **Software**

- Xorg version: **Cygwin_1.16.3**
- OpenGL acceleration: **Software**

In MobaXterm: Menu ``Sessions > New session > tab Shell > Terminal "Ubuntu bash (WSL)" > OK``

``Sessions > New session > tab Shell > Terminal "Ubuntu bash (WSL)" > OK``

Sessions > New session > tab Shell > Terminal "Ubuntu bash (WSL)" > OK

In MobaXterm: In the session lists, select the new **"Ubuntu Bash"** session

In bash terminal: type:

     sudo apt-get update && sudo apt-get dist-upgrade

to upgrade all the packages in Ubuntu

In the bash terminal: type:

     export DISPLAY=:0

to send the X11 windows to the local MobaXterm X server (add this line to your ``.bashrc`` to save time in the future)

to send the X11 windows to the local MobaXterm X server (add this line to your 

In the bash terminal: Type ``firefox``, then download and install `BrainVISA for Ubuntu 16.04 <#download>`_.

In bash terminal: Remove the BrainVISA version of ``libxcb`` to avoid the errors ``"libxcb-dri3.so.0: undefined symbol: xcb_send_fd"``:

     rm brainvisa-4.6.0/lib/libxcb*

In bash terminal: If you have additional errors, you may also try removing the BrainVISA version of ``libgcc_s``, ``libpcre``, ``libstdc++``, ``libtinfo`` (you may have to install these packages manually):

     sudo apt install gcc g++ libtinfo-dev libpcre++-dev

In bash terminal: If you have additional errors, you may also try removing the BrainVISA version of 

Error message /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0: undefined symbol: xcb_send_fd
If you see this message your system needs a more recent libxcb library than the one provided in the BrainVISA package.
To fix this, you can either try another BrainVISA package build on a more recent system (see the glibc version on the package name) or remove all the files starting with ``libxcb`` from the  ``lib`` directory of the BrainVISA package.

To fix this, you can either try another BrainVISA package build on a more recent system (see the glibc version on the package name) or remove all the files starting with 

:doc:`Outils pour la neuroimagerie disponibles pour la communauté <applications>`

.. |morphologist| raw:: html

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

<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

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

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

.. |anatomist| raw:: html

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

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

.. |brainrat| raw:: html

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

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

.. |ric| raw:: html

      <a href="applications.html#ric">
        <img src="http://www.mdbrain.org/personalpages/peter/front_image.jpg" style="height: 200px;" />
      </a>
    </div>

  <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

      <a href="applications.html#vobi_one">
        <img src="_static/images/vobi_one.png" style="height: 200px;" />
      </a>
    </div>

  <a href="applications.html#vobi_one">
    <img src="_static/images/vobi_one.png" style="height: 200px;" />
  </a>
</div>

.. |intranat| raw:: html

      <a href="applications.html#intranat">
        <img src="https://gin11-web.ujf-grenoble.fr/wp-content/uploads/2014/07/locateElectrodes2_anon.png" style="height: 200px;" />
      </a>
    </div>

  <a href="applications.html#intranat">
    <img src="https://gin11-web.ujf-grenoble.fr/wp-content/uploads/2014/07/locateElectrodes2_anon.png" style="height: 200px;" />
  </a>
</div>

.. |snapbase| raw:: html

        <img src="images/snapbase.jpg" style="height: 200px;" />
      </a>
    </div>

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

.. |datamind| raw:: html

        <img src="images/datamind.png" style="height: 200px;" />
      </a>
    </div>

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

:doc:`Segmentation du cerveau et analyse sulcale <morphologist>`

:doc:`Epaisseur corticale, index de gyrification... <applications>`

:ref:`Automatisation de vues de grandes bases de données <snapbase>`

.. |constellation| raw:: html

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

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

.. |disco| raw:: html

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

  <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

image:: _static/images/capsul.jpg

.. |highres| raw:: html

      <a href="demos_wip.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>

  <a href="demos_wip.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>

.. |nuclearimaging| raw:: html

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

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

.. |baby| raw:: html

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

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

.. |primate| raw:: html

      <a href="demos_wip.html#primate">
        <img src="images/primate.png" style="width: 300px;" />
      </a>
    </div>

  <a href="demos_wip.html#primate">
    <img src="images/primate.png" style="width: 300px;" />
  </a>
</div>

.. |connectomist| raw:: html

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

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

.. |sacha| raw:: html

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

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

.. |whasa| raw:: html

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

  <a href="demos_wip.html#whasa">
  </a>
</div>

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

image:: _static/images/axon_schema.jpg

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

image:: images/cort_toolbox.png

<table class="centered-cols docutils" style="width: 100%;">
  <colgroup>
  <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>
        Le projet <a href="http://cati-neuroimaging.com">CATI Neuroimaging</a>, plateforme d’analyse pour les maladies neurodégénératives, a basé une partie de ses chaînes de traitement et boîtes à outil sur l’infrastructure de BrainVISA
      </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=""/>
      </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>
  </tbody>
</table>

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

.. image:: images/cort.png
    :target: search.html

.. |english| image:: images/english.png
  :height: 20
  :target: index.html

<form class="search_box" action="https://www.google.com/cse" method="get">
  <input type="hidden" name="url" value="brainvisa.info" />
  <input type="hidden" name="cref" value="https://www.google.com/cse/tools/makecse?url=brainvisa.info" />
  <input type="hidden" name="ie" value="" />
  <input class="search_field" type="text" name="q" value="" />
  <input class="submit_btn" type="image" src="images/find_read.png" alt="Submit" />
</form>

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

<img src="http://www.mdbrain.org/personalpages/peter/front_image.jpg" style="height: 200px;" />

<img src="_static/images/vobi_one.png" style="height: 200px;" />

        <img src="https://f-tract.eu/wp-content/uploads/2016/05/logoIntrAnat.png" style="height: 200px;" />
      </a>
    </div>

    <img src="https://f-tract.eu/wp-content/uploads/2016/05/logoIntrAnat.png" style="height: 200px;" />
  </a>
</div>

      </a>
    </div>

  <a href="tools.html#highres-cortex-lamintion-of-the-cortex">
  </a>
</div>

      </a>
    </div>

  <a href="tools.html#primate">
  </a>
</div>

:doc:`Morphologist: Brain segmentation and sulcal analysis <morphologist>`

    <td>
        </a>
          </a><br/>
          </a><br/>
          </a>
        </div>
      </div>
      </p>
    </td>
    <td>
      </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>
      </p>
    </td>
    <td>
        <img src="images/labs/cnrs.png" style=""/></a>
      </div>
      </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>

.. |cite| raw:: html

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

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

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

image:: images/francais.png

<style>
}

}

}

}

}

}

}

}
</style>
  <div id="bv_carousel_axon_big" class="carousel slide auto" data-interval="5000" align="center" >
      <li data-target="#bv_carousel_axon_big" data-slide-to="0" class="active"></li>
      <li data-target="#bv_carousel_axon_big" data-slide-to="1"></li>
    </ol>
            <img align="center" src="_static/images/axon_gui.jpg" style="max-height: 492px; max-width: 692px;" />
      </div>
          <img align="center" src="_static/images/axon_schema.jpg" />
      </div>

    </div>
    <a class="carousel-control left" href="#bv_carousel_axon_big" data-slide="prev">&lsaquo;</a>
    <a class="carousel-control right" href="#bv_carousel_axon_big" data-slide="next">&rsaquo;</a>
    <script>$("#bv_carousel_axon_big").carousel();</script>
  </div>
</div>

BrainVISA provides a complete, modular, infrastructure for neuroimaging software. It helps organizing heterogeneous software and data and provides a common general graphical interface for users.

:axonusr:`Axon <index.html>` is the name of the software which runs when you use the ``brainvisa`` command. The latter is still named ``brainvisa`` for historical reasons. It is a central software in the BrainVISA environment.

 for historical reasons. It is a central software in the BrainVISA environment.

.. image:: _static/images/axon_schema.jpg

:ref:`Data organization as directory trees with database indexing and querying <axon_data_management>`

Data organization as directory trees with database indexing and querying

:doc:`Portfolio of applicative toolboxes ready for use <applications>`

:ref:`Software glue for various neuroimaging processing software, including tools developed by the team labs contributing to BrainVISA, and external software <axon_software>`

Software glue for various neuroimaging processing software, including tools developed by the team labs contributing to BrainVISA, and external software

:ref:`Interactive 3D visualization for all kind of neuroimaging data <axon_visu>`, supporting a wide range of data file formats: :doc:`anatomist`

:ref:`Interactive 3D visualization for all kind of neuroimaging data <axon_visu>`

:ref:`Multiprocessor computing infrastructure, allowing distributed computing both on a local computer or a remote computing resource (cluster) <axon_processing>`

Multiprocessor computing infrastructure, allowing distributed computing both on a local computer or a remote computing resource (cluster)

:ref:`Software integration tools allowing to develop or interface new processing tools <integrate>`

Software integration tools allowing to develop or interface new processing tools

`Software packaging and distribution tools allowing users to easily download, install and use various toolboxes <#distributing-tools-to-the-community>`_

Software packaging and distribution tools allowing users to easily download, install and use various toolboxes

software packaging and distribution tools allowing users to easily download, install and use various toolboxes

`Lower-level neuroimaging software libraries <#developing-image-analysis-algorithms>`_ (:aimsusr:`AIMS <index.html>`) useable as building blocks for new processing tools

`Lower-level neuroimaging software libraries <#developing-image-analysis-algorithms>`_

<div style="display: block; text-align: center; margin: 10px;">
  <img src="images/bv_infrastructure.png" style="width: 600px;" usemap="#infra_map" />
  <map id="infra_map" name="infra_map">
    <area shape="rect" coords="0,0,158,130" href="#integrate" />
    <area shape="rect" coords="214,0,372,130" href="applications.html" />
    <area shape="rect" coords="427,62,600,236" href="#distributing-tools-to-the-community" />
    <area shape="rect" coords="0,164,158,294" href="#axon" />
    <area shape="rect" coords="214,170,372,302" href="#packaging-and-installation-system" />
  </map>
</div>
<div style="display: block; text-align: center;">
  <div style="display: inline-block; width: 650px;">
    BrainVISA provides a complete software environment, handling the whole chain from developing processing tools to the end user, via packaging and distribution steps.
  </div>
</div>

Axon provides a graphical user environment, and integrates the different tools and data to make them available for end users.

  <img src="images/axon_organisation_overview.png" style="width: 600px;" usemap="#axon_map" />
  <map id="axon_map" name="axon_map">
    <area shape="rect" coords="88,0,538,55" href="#axon-gui" />
    <area shape="rect" coords="88,62,538,115" href="applications.html" />
    <area shape="rect" coords="88,125,234,178" href="#axon-data-management" />
    <area shape="rect" coords="240,125,385,178" href="#axon-visu" />
    <area shape="rect" coords="391,125,538,178" href="#axon-software" />
    <area shape="rect" coords="88,210,538,265" href="#axon-processing" />
  </map>
</div>
    The different software components assembled in the Axon software.
  </div>
</div>

:axonusr:`General documentation <index.html>`
  * :axonusr:`Tutorial <tutorial.html>`
  * :axonusr:`Complete manual <axon_manual.html>`
  * :axon:`Introduction slides <intro_bv.pdf>`
  * :axon:`GUI embedded main user documentation <en/help/index.html>`

* :axonusr:`Tutorial <tutorial.html>`
* :axonusr:`Complete manual <axon_manual.html>`
* :axon:`Introduction slides <intro_bv.pdf>`
* :axon:`GUI embedded main user documentation <en/help/index.html>`

:axon:`GUI embedded main user documentation <en/help/index.html>`

Axon organizes processing tools and provides a unified graphical user interface for them.

This user interfaces are automatically generated by Axon from processes parameters characteristics.

However custom user interfaces are also possible and used in some applications, such as :morphouiusr:`Morphologist UI <index.html>`.

However custom user interfaces are also possible and used in some applications, such as 

Data is kept in organized directories, and referenced in databases. Files organization can be described to adapt a particular schema, for instance to allow reusing data from external sofftware such as Freesurfer_ or SPM_. Databasing allows to query and filter data to be processed, and to generate processed file names.

Data is kept in organized directories, and referenced in databases. Files organization can be described to adapt a particular schema, for instance to allow reusing data from external sofftware such as 

. Databasing allows to query and filter data to be processed, and to generate processed file names.

In addition to files organization, Axon offers a way of automatically handling the complex problem of coordinates systems used by various data.

See :axonusr:`The documentation <axon_manual2.html#databases-and-ontologies>` for more details.

Different software can be interfaced with BrainVISA and Axon, even when they are using different languages and different conventions, coordinates systems, data organization...

Different software can be interfaced with BrainVISA and Axon, even when they are using different languages and different conventions, coordinates systems, data organization…

Several BrainVISA toolboxes are already interfacing some popular software from the neuroimaging community, at least part of their tools: FreeSurfer_, SPM_, FSL_... Other tools and software may be interfaced the same way via extensions.

Several BrainVISA toolboxes are already interfacing some popular software from the neuroimaging community, at least part of their tools: 

… Other tools and software may be interfaced the same way via extensions.

Many software libraries are directly useable from BrainVISA toolboxes and processing tools, amongst which several external Python language libraries which prove very useful for the neuroimaging community: for instance Numpy_, Scipy_, Matplotlib_, and many others.

Many software libraries are directly useable from BrainVISA toolboxes and processing tools, amongst which several external Python language libraries which prove very useful for the neuroimaging community: for instance 

.. image:: _static/images/grasping_3D-sulci.jpg
    :height: 300

Visualization and interactive edition of data is integrated in Axon user interface, via the eye |eye| and pencil |pencil| icons close to data parameters in processing interfaces.

Visualization and interactive edition of data is integrated in Axon user interface, via the eye 

Axon provides facilities to customize and write new specialized visualization tools. Most of them make use of :doc:`anatomist`. Visualization can be adapted to specific needs for specific data, and complete 3D scenes can be built and triggered by a simple click.

Axon provides facilities to customize and write new specialized visualization tools. Most of them make use of 

. Visualization can be adapted to specific needs for specific data, and complete 3D scenes can be built and triggered by a simple click.

Moreover coordinates systems are transparently and automatically managed by the combination of Axon databasing and Anatomist visualization capabilities.

Axon provides a processing pipeline management infrastructure: processes are organized with dependencies, allowing parallel execution.

Parallel or distributed execution may be performed either locally (on a mutiprocessor machine for instance), or remotely on a computing cluster. Distributed processing is managed via :soma_workflow_gen:`Soma-Workflow <index.html>`. This software library handles jobs dependencies and distribution, and interfaces in a transparent way remote computing clusters using various batch systems, or a local machine.

Parallel or distributed execution may be performed either locally (on a mutiprocessor machine for instance), or remotely on a computing cluster. Distributed processing is managed via 

. This software library handles jobs dependencies and distribution, and interfaces in a transparent way remote computing clusters using various batch systems, or a local machine.

BrainVISA is designed to be customizable and extensible. User-defined research tools can be easily added either for personal convenience, for sharing research tools in a lab, or to distribute finalized toolboxed to the community.

All infrastructure software is free and works on Linux, Mac OS and Windows. Some additional toolboxes may contain non-free code and/or be limited to fewer platforms, but are out of topic here.

The levels correspond to different layers of the infrastructure, which may be schematically represented this way:

  <img src="images/bv_dev_schema.png" style="width: 600px;" usemap="#dev_map" />
  <map id="dev_map" name="dev_map">
    <area shape="rect" coords="0,0,600,70" href="../axon/dev_doc/index.html" />
    <area shape="rect" coords="0,108,600,178" href="#toolboxes" />
    <area shape="rect" coords="0,322,138,392" href="../index_commands.html" />
    <area shape="rect" coords="160,213,315,283" href="../pyaims/sphinx/index.html" />
    <area shape="rect" coords="169,322,305,392" href="../aimsdata/user_doc/index.html" />
    <area shape="rect" coords="333,213,455,283" href="anatomist.html" />
    <area shape="rect" coords="470,213,600,283" href="https://python.org" />
  </map>
</div>

More details may be found in the following sections, which may become very technical.

:ref:`An overview of the different programming tools <devtools>`

.. image:: images/cort_toolbox.png
    :width: 96

BrainVISA is a modular environment. It is possible to install, use, and build on a subset of the tools. Of course there are dependencies between elements but large parts are optional.

<div style="display: inline; text-align: center;">
<div style="display: inline-block; margin: 20px;">

.. figure:: images/dev_usecase_commands.png
    :width: 300

    Low-level: use image processing commands and C++ libraries

.. figure:: images/dev_usecase_python.png

    Image processing, with Python scripting

.. figure:: images/dev_usecase_visu.png

    Visualization only

.. figure:: images/dev_usecase_axon.png

    Axon, without visualization or builtin processing toolboxes

.. |axon| raw:: html

    <div style="position: relative; top: -20px;"><img class="white_circle align-left" src="images/brainvisa_large.png" style="width: 90px;"/></div>

<div style="position: relative; top: -20px;"><img class="white_circle align-left" src="images/brainvisa_large.png" style="width: 90px;"/></div>

Adding processes may be done easily using a standard binary installation of BrainVISA: no need to access the source code of projects and to compile anything.

Processes may be added in a personal directory which is seen as a regular toolbox. Thus adding a personal process is just a matter of adding a Python script file in this processes directory.

The :axon:`Programming course slides <Programming_with_brainvisa.pdf>` with corresponding :axon:`data <Programming_with_brainvisa.zip>` are a good starting point.

This is done within the :axonusr:`Axon framework <index.html>`, using its :axondev:`programming interface <index.html>`.

Toolboxes are a set of organized Axon processes, and may also contain types and files oprganization definitions, and documentation. They are also described in the :axon:`Programming course slides <Programming_with_brainvisa.pdf>`.

Toolboxes are a set of organized Axon processes, and may also contain types and files oprganization definitions, and documentation. They are also described in the 

BrainVISA provides image analysis libraries, which are mostly focused on anatomical MRI processing but may be used in various applications. They handle various types of data used in the field of neuroimaging, and unserstand a rather large set of file formats. These are the :aimsdata:`AIMS libraries <user_doc/index.html>`. They include a set of C++ language libraries, some Python language bindings which make them scriptable in an easy way, and executable programs which may be direcly called by users or by scripts.

BrainVISA provides image analysis libraries, which are mostly focused on anatomical MRI processing but may be used in various applications. They handle various types of data used in the field of neuroimaging, and unserstand a rather large set of file formats. These are the 

. They include a set of C++ language libraries, some Python language bindings which make them scriptable in an easy way, and executable programs which may be direcly called by users or by scripts.

Programming in C++ allows lower-level, optimized image processing algorithms to be written. However this is at the cost of requiring compilation.
There is a new tool to help developing and distributing tools: see :casadistro:`Casa-distro <index.html>`. This tool allows to get libraries and compilation tools in Docker containers, so that they can be compiled and redistributed in an environment which is compatible with BrainVisa public binary distributions.

There is a new tool to help developing and distributing tools: see 

. This tool allows to get libraries and compilation tools in Docker containers, so that they can be compiled and redistributed in an environment which is compatible with BrainVisa public binary distributions.

At lower level, the libraries are not available as binary installable files on every system, developing for compilation generally requires to compile the AIMS libraries from sources. Thus you will have to look at the :ref:`sources repository section <sources>` and the :ref:`build system section <building>`.

At lower level, the libraries are not available as binary installable files on every system, developing for compilation generally requires to compile the AIMS libraries from sources. Thus you will have to look at the 

.. image:: _static/images/fusion_cutmesh_2.png
    :width: 96

Visualization in BrainVISA can be provided via :axonusr:`Axon <index.html>` through viewer processes. Most of them are making use of :doc:`Anatomist <anatomist>` for its interactive 3D capabilities, and its easy scripting facilities: :pyanatomist:`PyAnatomist <index.html>` for scripting in Python language.

 for its interactive 3D capabilities, and its easy scripting facilities: 

.. image:: _static/images/cort_news.png
    :width: 96

Tools based on BrainVISA development libraries can be freely distributed to the community. Distribution may be done via software packages which can be installed on top of existing BrainVISA installations, just as in the :doc:`download section <download>`.

Tools based on BrainVISA development libraries can be freely distributed to the community. Distribution may be done via software packages which can be installed on top of existing BrainVISA installations, just as in the 

From version 4.5, BrainVISA is installed via a modular installer tool, similar to what is commonly found to manage software packages in a Linux distribution, but which works on all supported architectures (Linux, Mac, Windows), and allowing local installations: not needed administrator priviledges, and multiple versions of BrainVISA may be installed independently in different user directories.

It is possible to build custom packages in custom repositories, which can be added to the installer.

Details are available in the `Packaging and installation system`_ section.

Toolboxes developers have some degrees of freedom on the licenses under which they can distribute their software. There are a few limitations, however:

**Python graphical interfaces are** GPL_ (CeCILL-v2_): these graphical parts are built using PyQt_, which is bound to GPL_, and thus require all software built on them to be also distributed under a GPL-compatible licence. This applies to all Axon processes, which may appear in the brainvisa GUI.

, and thus require all software built on them to be also distributed under a GPL-compatible licence. This applies to all Axon processes, which may appear in the brainvisa GUI.

But lower-level processing tools do not normally require such graphical interface, so are not bound to a specific license. Toolbox designers are thus free to choose the distribution license they prefer, provided their toolbox is separated in two distinct parts: the processing part (non-GUI, any license may be chosen), and the Axon part (GPL or CeCILL-v2).

Anatomist also has Qt user interface, but is globally built in C++ so does not have a strong dependency on PyQt: Anatomist is distributed under the CeCILL-B license (BSD-like). It has plugins in Python language, which may make use of PyQt however.

PyAnatomist, and python plugins, are using PyQt, so is distributed under the CeCILL-v2 (GPL-compatible) license. Custom anatomist plugins in Python must thus follow this licensing policy.

A new tool has been designed to setup very quickly a new developer into a situation when he can start writing, building and testing tools, without the burden of setting up a complete development system: this is :casadistro:`Casa-distro <index.html>`. It will also ensure to build toolboxes and new tools that are compatible with public distributions of BrainVisa.

A new tool has been designed to setup very quickly a new developer into a situation when he can start writing, building and testing tools, without the burden of setting up a complete development system: this is 

. It will also ensure to build toolboxes and new tools that are compatible with public distributions of BrainVisa.

.. |axon_small| image:: images/brainvisa_large.png
    :height: 48
    :target: infrastructure.html

image:: images/brainvisa_large.png

.. |anatomist_small| image:: _static/images/fusion_cutmesh_2.png
    :target: anatomist.html

image:: _static/images/fusion_cutmesh_2.png

.. |soma_workflow_small| image:: images/soma_workflow_icon.png
    :target: soma/soma-workflow/index.html

image:: images/soma_workflow_icon.png

.. |capsul_small| image:: _static/images/capsul.jpg

All of the software here is free and portable on Linux, Mac and Windows. Some additional toolboxes may contain non-free code and/or be limited to fewer platforms, but are not listed here.

.. |axon_head| replace:: |axon_small| :doc:`Axon, conductor software <infrastructure>`

.. |anatomist_head| replace:: |anatomist_small| :ref:`Anatomist 3D interactive visualization <anatomist_dev>`

.. |soma_workflow_head| replace:: |soma_workflow_small| :soma_workflow_gen:`Distributed processing: Soma-Workflow <index.html>`

.. |aimsdata_head| replace:: :aimsdata:`AIMS image processing <user_doc/index.html>`

.. |somabase_head| replace:: :somabase:`Soma-base <sphinx/index.html>`

.. |capsul_head| replace:: |capsul_small| :capsul:`CAPSUL <index.html>` pipelining system

.. |casa_distro_head| replace:: :casadistro:`Casa-Distro <index.html>` development and distribution environment

.. |bv_cmake_head| replace:: :bv-cmake:`Brainvisa-Cmake <index.html>` build environment

.. |installer_head| replace:: :installer:`Brainvisa-Installer <index.html>` packaging, installer and repository tools

the "brainvisa" program and libraries, pipelining infrastructure, databasing, and graphical interface. Language: Python

the “brainvisa” program and libraries, pipelining infrastructure, databasing, and graphical interface. Language: Python

* :pyanatomist:`PyAnatomist <index.html>`
* :anadox:`C++ library <index.html>`

* :pyaims:`PyAims, in Python <index.html>`
* :aimsdox:`C++ library and commands <index.html>`

development setup in Docker machines with packaging and distribution facilities.

.. image:: images/cort_install.png
    :width: 96

Two repositories are used to host the source code of BrainVISA project. All components with public source code are on `GitHub
<https://github.com/>`_ (either on `BrainVISA organization
<https://github.com/brainvisa/>`_ or on `Populse organization
<https://github.com/populse/>`_). Project with restricted read access are hosted on `BioProj
<https://bioproj.cea.fr/redmine/projects/brainvisa>`_, the historical BrainVISA RedMine server. BioProj is operated by the CEA institution, and has access rules that forbids anonymous access. A login and password are mandatory to access to projects on BioProj. However there is a "public" login/password to access the open-source code that is still on BioProj (migration to GitHub is ongoing):

Two repositories are used to host the source code of BrainVISA project. All components with public source code are on 

, the historical BrainVISA RedMine server. BioProj is operated by the CEA institution, and has access rules that forbids anonymous access. A login and password are mandatory to access to projects on BioProj. However there is a “public” login/password to access the open-source code that is still on BioProj (migration to GitHub is ongoing):

So it is normally possible to access the repository using this kind of link:

A GitHub project also holds some developers documentation:
https://github.com/brainvisa/brainvisa.github.io

Projects are mainly in C++ and Python language. As BrainVISA is modular, it is made of multiple projects, which are separated by scope, aim, maintainers, language, and licence. To build the whole thing, we needed a tool to build an aggregation of the various projects. This tool is based on `CMake <https://cmake.org>`_ but needed a higher-level tool to glue the various projects. This is the role of the :bv-cmake:`brainvisa-cmake project <index.html>` of BrainVisa, and its main program, :bv-cmake:`bv_maker <bv_maker.html>`.

Projects are mainly in C++ and Python language. As BrainVISA is modular, it is made of multiple projects, which are separated by scope, aim, maintainers, language, and licence. To build the whole thing, we needed a tool to build an aggregation of the various projects. This tool is based on 

 but needed a higher-level tool to glue the various projects. This is the role of the 

Instructions on how to use it are available on the sources server web interface:

:bv-cmake:`How to compile BrainVISA projects <compile_existing.html>`

The building tools integrate software source repositories management, configuration, building, documentation generation, automatic testing, and software packaging. They thus allow to be used as a complete integrated development process.

As an example we have them running automatically every night on 7 different systems (Windows, Mac, and a set of Linux variants, including both virtual and physical machines). Problems are notified to the maintainers.

The packaging / installation software is documented here: :installer:`BrainVISA Installer <index.html>`.

It allows to generate a packages repository, and the :ref:`installer program available in the download section <install>`.

:ref:`installer program available in the download section <install>`

Brainvisa-installer can also be used via :bv-cmake:`bv_maker <index.html>` which is generally mmore convenient since it allows to store all configuration and options in a config file.

 which is generally mmore convenient since it allows to store all configuration and options in a config file.

:morpho_api:`Morphoplogist CAPSUL processes APIs <index.html>`: Morphologist processes constituting the main Morphologist pipeline have been converted to the new CAPSUL API.

: Morphologist processes constituting the main Morphologist pipeline have been converted to the new CAPSUL API.

<table class="docutils">
  <thead>
    <tr class="row-odd">
      <th>Project component:</th>
      <th>repos type:</th>
      <th>repository URL:</th>
    </tr>
  </thead>
  <tbody>
    <tr class="row-even">
      <td colspan="3"><b>opensource components:</b></td>
    </tr>
      <td>aims-free</td>
      <td>git</td>
      <td><a href="https://github.com/brainvisa/aims-free.git">https://github.com/brainvisa/aims-free.git</a></td>
    </tr>
      <td>aims-gpl</td>
      <td><a href="https://github.com/brainvisa/aims-gpl.git">https://github.com/brainvisa/aims-gpl.git</a></td>
    </tr>
      <td>anatomist-free</td>
      <td><a href="https://github.com/brainvisa/anatomist-free.git">https://github.com/brainvisa/anatomist-free.git</a></td>
    </tr>
      <td>anatomist-gpl</td>
      <td><a href="https://github.com/brainvisa/anatomist-gpl.git">https://github.com/brainvisa/anatomist-gpl.git</a></td>
    </tr>
      <td>axon</td>
      <td><a href="https://github.com/brainvisa/axon.git">https://github.com/brainvisa/axon.git</a></td>
    </tr>
      <td>brainvisa-cmake</td>
      <td><a href="https://github.com/brainvisa/brainvisa-cmake.git">https://github.com/brainvisa/brainvisa-cmake.git</a></td>
    </tr>
      <td>brainvisa-share</td>
      <td><a href="https://github.com/brainvisa/brainvisa-share.git">https://github.com/brainvisa/brainvisa-share.git</a></td>
    </tr>
      <td>brainvisa-spm</td>
      <td><a href="https://github.com/brainvisa/brainvisa-spm.git">https://github.com/brainvisa/brainvisa-spm.git</a></td>
    </tr>
      <td>brainvisa_freesurfer</td>
      <td><a href="https://github.com/brainvisa/brainvisa_freesurfer.git">https://github.com/brainvisa/brainvisa_freesurfer.git</a></td>
    </tr>
      <td>capsul</td>
      <td><a href="https://github.com/populse/capsul.git">https://github.com/populse/capsul.git</a></td>
    </tr>
      <td>casa-distro</td>
      <td><a href="https://github.com/brainvisa/casa-distro.git">https://github.com/brainvisa/casa-distro.git</a></td>
    </tr>
      <td>cortical_surface-gpl</td>
      <td><a href="https://github.com/brainvisa/cortical_surface-gpl.git">https://github.com/brainvisa/cortical_surface-gpl.git</a></td>
    </tr>
      <td>highres-cortex</td>
      <td><a href="https://github.com/neurospin/highres-cortex.git">https://github.com/neurospin/highres-cortex.git</a></td>
    </tr>
      <td>morpho-deepsulci</td>
      <td><a href="https://github.com/brainvisa/morpho-deepsulci.git">https://github.com/brainvisa/morpho-deepsulci.git</a></td>
    </tr>
      <td>morphologist-gpl</td>
      <td><a href="https://github.com/brainvisa/morphologist-gpl.git">https://github.com/brainvisa/morphologist-gpl.git</a></td>
    </tr>
      <td>morphologist-ui</td>
      <td><a href="https://github.com/brainvisa/morphologist.git">https://github.com/brainvisa/morphologist.git</a></td>
    </tr>
      <td>populse_db</td>
      <td><a href="https://github.com/populse/populse_db.git">https://github.com/populse/populse_db.git</a></td>
    </tr>
      <td>soma-base</td>
      <td><a href="https://github.com/populse/soma-base.git">https://github.com/populse/soma-base.git</a></td>
    </tr>
      <td>soma-io</td>
      <td><a href="https://github.com/brainvisa/soma-io.git">https://github.com/brainvisa/soma-io.git</a></td>
    </tr>
      <td>soma-workflow</td>
      <td><a href="https://github.com/populse/soma-workflow.git">https://github.com/populse/soma-workflow.git</a></td>
    </tr>
      <td colspan="3"><b>restricted access components:</b></td>
    </tr>
      <td>bioprocessing</td>
      <td><a href="https://bioproj.extra.cea.fr/git/bioprocessing">https://bioproj.extra.cea.fr/git/bioprocessing</a></td>
    </tr>
      <td>brainrat-gpl</td>
      <td><a href="https://bioproj.extra.cea.fr/git/brainrat-gpl">https://bioproj.extra.cea.fr/git/brainrat-gpl</a></td>
    </tr>
      <td>brainrat-private</td>
      <td><a href="https://bioproj.extra.cea.fr/git/brainrat-private">https://bioproj.extra.cea.fr/git/brainrat-private</a></td>
    </tr>
      <td>catidb-client</td>
      <td><a href="https://github.com/cati-neuroimaging/catidb-client.git">https://github.com/cati-neuroimaging/catidb-client.git</a></td>
    </tr>
      <td>constellation-gpl</td>
      <td><a href="https://github.com/brainvisa/constellation-gpl.git">https://github.com/brainvisa/constellation-gpl.git</a></td>
    </tr>
      <td>constellation-nonfree</td>
      <td><a href="https://github.com/brainvisa/constellation-nonfree.git">https://github.com/brainvisa/constellation-nonfree.git</a></td>
    </tr>
      <td>cortical_surface-nonfree</td>
      <td><a href="https://github.com/brainvisa/cortical_surface-nonfree.git">https://github.com/brainvisa/cortical_surface-nonfree.git</a></td>
    </tr>
      <td>deidentification</td>
      <td><a href="https://github.com/cati-neuroimaging/deidentification.git">https://github.com/cati-neuroimaging/deidentification.git</a></td>
    </tr>
      <td>disco</td>
      <td><a href="https://bioproj.extra.cea.fr/git/brainvisa-disco">https://bioproj.extra.cea.fr/git/brainvisa-disco</a></td>
    </tr>
      <td>longitudinal_pipelines</td>
      <td><a href="https://github.com/cati-neuroimaging/longitudinal_pipelines.git">https://github.com/cati-neuroimaging/longitudinal_pipelines.git</a></td>
    </tr>
      <td>morphologist-baby</td>
      <td><a href="https://bioproj.extra.cea.fr/git/brainvisa-t1mri/morphologist-baby.git">https://bioproj.extra.cea.fr/git/brainvisa-t1mri/morphologist-baby.git</a></td>
    </tr>
      <td>morphologist-nonfree</td>
      <td><a href="https://github.com/brainvisa/morphologist-nonfree.git">https://github.com/brainvisa/morphologist-nonfree.git</a></td>
    </tr>
      <td>nuclear_imaging-gpl</td>
      <td><a href="https://github.com/cati-neuroimaging/nuclear_imaging-gpl.git">https://github.com/cati-neuroimaging/nuclear_imaging-gpl.git</a></td>
    </tr>
      <td>nuclear_imaging-nonfree</td>
      <td><a href="https://github.com/cati-neuroimaging/nuclear_imaging-nonfree.git">https://github.com/cati-neuroimaging/nuclear_imaging-nonfree.git</a></td>
    </tr>
      <td>preclinical-imaging-iam</td>
      <td><a href="https://bioproj.extra.cea.fr/git/preclinical-imaging-iam">https://bioproj.extra.cea.fr/git/preclinical-imaging-iam</a></td>
    </tr>
      <td>primatologist-gpl</td>
      <td><a href="https://bioproj.extra.cea.fr/git/primatologist-gpl">https://bioproj.extra.cea.fr/git/primatologist-gpl</a></td>
    </tr>
      <td>qualicati</td>
      <td><a href="https://github.com/cati-neuroimaging/qualicati.git">https://github.com/cati-neuroimaging/qualicati.git</a></td>
    </tr>
      <td>rsfmri</td>
      <td><a href="https://github.com/cati-neuroimaging/rsfmri.git">https://github.com/cati-neuroimaging/rsfmri.git</a></td>
    </tr>
      <td>sacha-gpl</td>
      <td><a href="https://github.com/cati-neuroimaging/sacha-gpl.git">https://github.com/cati-neuroimaging/sacha-gpl.git</a></td>
    </tr>
      <td>sacha-nonfree</td>
      <td><a href="https://github.com/cati-neuroimaging/sacha-nonfree.git">https://github.com/cati-neuroimaging/sacha-nonfree.git</a></td>
    </tr>
      <td>sulci-nonfree</td>
      <td><a href="https://github.com/brainvisa/sulci-nonfree.git">https://github.com/brainvisa/sulci-nonfree.git</a></td>
    </tr>
      <td>whasa-gpl</td>
      <td><a href="https://github.com/cati-neuroimaging/whasa-gpl.git">https://github.com/cati-neuroimaging/whasa-gpl.git</a></td>
    </tr>
      <td>whasa-nonfree</td>
      <td><a href="https://github.com/cati-neuroimaging/whasa-nonfree.git">https://github.com/cati-neuroimaging/whasa-nonfree.git</a></td>
    </tr>
  </tbody>
<table>

IFR49, CEA/SAC/DSV/I2BM/NeuroSpin, Bât 145 Point Courrier 156, F-91191 GIF/YVETTE FRANCE
Phone : +33 1 69 08 65 21

* Denis Riviere, researcher in CEA
* Yann Cointepas, researcher in CEA

<style>
}

}

}

}

}

}

}

}
</style>
    </ol>
            <img align="center" src="_static/images/morphologist-ui.jpg" style="max-height: 492px; max-width: 692px;" />
      </div>
      </div>
      </div>

    </div>
  </div>
</div>

older :    <!--#include file="carousels/car_morphologist_big.html" -->

C. Fischer, G. Operto, S. Laguitton, M. Perrot, I. Denghien, D. Rivière, and J.-F. Mangin: **Morphologist 2012: the new morphological pipeline of BrainVISA**, In *Proc. HBM*, 2012.

Fischer, G. Operto, S. Laguitton, M. Perrot, I. Denghien, D. Rivière, and J.-F. Mangin: **Morphologist 2012: the new morphological pipeline of BrainVISA**, In *Proc. HBM*, 2012.

Fischer, G. Operto, S. Laguitton, M. Perrot, I. Denghien, D. Rivière, and J.-F. Mangin: 

**Morphologist 2012: the new morphological pipeline of BrainVISA**

:morpho:`A more complete doc is available here <user_doc/index.html>`

Morphologist now has a new graphical interface, featuring simplified user experience and quick interactive visualization:

.. image:: _static/images/morphologist-ui.jpg
    :width: 50%
    :target: ../morphologist-ui/index.html

It can be run either as a standalone program (``morphologist``), or through BrainVISA.

Slides on the :morphologist:`Morphologist pipeline <morphologist.pdf>`

:morphoproc:`Morphologist toolbox documentation <categories/morphologist/category_documentation.html>`

Atlas view in 3D: `see this little demo <webgl_demo/webgl.html>`_

This atlas gives the probability of finding various cortical folds or gray nuclei across a population.

.. figure:: _static/images/bsa/anat_landmark_picture-2_small.jpg
    :target: _static/images/bsa/anat_landmark_picture-2.png

    Probability maps

    Probability maps corresponding to a few anatomical landmarks (cortical folds) overlaid on a T1 template

Probability maps corresponding to a few anatomical landmarks (cortical folds) overlaid on a T1 template

.. figure:: _static/images/bsa/atlas_sulci_small.jpg
    :target: _static/images/bsa/atlas_sulci.png

    Outlines

    The outline at 50% of all the structures

.. figure:: _static/images/bsa/nomenclature_small.jpg
    :target: _static/images/bsa/nomenclature.png

    Labels location

    Location of sulcal labels mapped on a 3D representation of a refined version of the anatomical atlas (after a sulcuswise non-linear registration scheme).

Location of sulcal labels mapped on a 3D representation of a refined version of the anatomical atlas (after a sulcuswise non-linear registration scheme).

.. figure:: _static/images/bsa/poster_hbm11_perrot_m_small.jpg
    :target: _static/images/bsa/poster_hbm11_perrot_m_150dpi.jpg

    HBM 2011 poster

    A high-resolution full-brain probabilistic atlas of regions based on cortical folds

A high-resolution full-brain probabilistic atlas of regions based on cortical folds

.. figure:: _static/images/bsa/nomenclature_translation_small.png
    :target: _static/images/bsa/nomenclature_translation.png

    Atlas of Sulci with nomenclature table (2018)

    Location of sulci named by their Brainvisa acronyms or their full anatomical names

Location of sulci named by their Brainvisa acronyms or their full anatomical names

`Download the Atlas <https://brainvisa.info/download/data/anat_landmark_atlas.nii.gz>`_ (nii.gz file, 71Mo, in MNI space, 2mm isotropic voxels)

`Download the Atlas <https://brainvisa.info/download/data/anat_landmark_atlas.nii.gz>`_

`Table giving the names of the anatomical structures <_static/images/bsa/anat_landmark_atlas.csv>`_ (csv file)

`Table giving the names of the anatomical structures <_static/images/bsa/anat_landmark_atlas.csv>`_

`CSV of anatomical structures <_static/images/bsa/anat_landmark_atlas.csv>`_ - fields : index, location (x,y,z), color(r,g,b), brainvisa acronym and anatomical label.

`CSV of anatomical structures <_static/images/bsa/anat_landmark_atlas.csv>`_

 - fields : index, location (x,y,z), color(r,g,b), brainvisa acronym and anatomical label.

`Table of sulcal labels <_static/images/bsa/anat_landmark_atlas_table.pdf>`_ - Meanings of Brainvisa acronyms used for sulcal structures

`Table of sulcal labels <_static/images/bsa/anat_landmark_atlas_table.pdf>`_

The :documents:`older sulci labels used before BrainVisa/Morphologist 3.2 <nomenclature/BV_nomenclature.pdf>`, and handled by the older ANN models 2001. There are slight changes, but there are changes.

, and handled by the older ANN models 2001. There are slight changes, but there are changes.

M. Perrot, D. Riviere, A. Tucholka, J.-F. Mangin : **Joint Bayesian Cortical Sulci Recognition and Spatial Normalization**, *IPMI* 2009 `paper <http://www.springerlink.com/content/kr237xh45132283u/>`_

Perrot, D. Riviere, A. Tucholka, J.-F. Mangin : **Joint Bayesian Cortical Sulci Recognition and Spatial Normalization**, *IPMI* 2009 `paper <http://www.springerlink.com/content/kr237xh45132283u/>`_

**Joint Bayesian Cortical Sulci Recognition and Spatial Normalization**

Joint Bayesian Cortical Sulci Recognition and Spatial Normalization

M. Perrot, D. Rivière, and J.-F. Mangin. **Cortical sulci recognition and spatial normalization**. *Medical Image Analysis* 2011 `paper <http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6W6Y-52BPK8B-1-3W&_cdi=6611&_user=2432700&_pii=S1361841511000302&_origin=&_coverDate=08%2F31%2F2011&_sk=999849995&view=c&wchp=dGLbVlz-zSkzk&md5=da7babd94f7373e9a907a63d9c57a035&ie=/sdarticle.pdf>`_

Perrot, D. Rivière, and J.-F. Mangin. **Cortical sulci recognition and spatial normalization**. *Medical Image Analysis* 2011 `paper <http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6W6Y-52BPK8B-1-3W&_cdi=6611&_user=2432700&_pii=S1361841511000302&_origin=&_coverDate=08%2F31%2F2011&_sk=999849995&view=c&wchp=dGLbVlz-zSkzk&md5=da7babd94f7373e9a907a63d9c57a035&ie=/sdarticle.pdf>`_

Alan Tucholka, Bertrand Thirion, Matthieu Perrot, Philippe Pinel, Jean-François Mangin and Jean-Baptiste Poline : **Probabilistic Anatomo-Functional Parcellation of the Cortex : How Many Regions ?**, *MICCAI* 2008 `paper <http://www.springerlink.com/content/qk36n3m522554367/>`_

Alan Tucholka, Bertrand Thirion, Matthieu Perrot, Philippe Pinel, Jean-François Mangin and Jean-Baptiste Poline : 

**Probabilistic Anatomo-Functional Parcellation of the Cortex : How Many Regions ?**

Probabilistic Anatomo-Functional Parcellation of the Cortex : How Many Regions ?

Merlin Keller, Marc Lavielle, Matthieu Perrot and Alexis Roche. **Anatomically Informed Bayesian Model Selection for fMRI Group Data Analysis**. *MICCAI* 2009 `paper <http://www.springerlink.com/content/u04520x4v0t17524/>`_

Merlin Keller, Marc Lavielle, Matthieu Perrot and Alexis Roche. 

**Anatomically Informed Bayesian Model Selection for fMRI Group Data Analysis**

Anatomically Informed Bayesian Model Selection for fMRI Group Data Analysis

Gaël Varoquaux, Alexandre Gramfort, Jean-Baptiste Poline, Bertrand Thirion. **Brain covariance selection : better individual functional connectivity models using population prior**. *NIPS* 2010 `link <https://arxiv.org/pdf/1008.5071>`_

Gaël Varoquaux, Alexandre Gramfort, Jean-Baptiste Poline, Bertrand Thirion. 

**Brain covariance selection : better individual functional connectivity models using population prior**

Brain covariance selection : better individual functional connectivity models using population prior

Much performance improvements in Soma-Workflow, the parallel execution tool.

We have stopped maintaining a complete bibliography list. You can look in pubmed or google scholar, for instance.

.. |riviere09| image:: images/pdf.png
    :target: https://brainvisa.info/download/papers/Riviere-HBM09.pdf

image:: images/pdf.png

D. Rivière, D. Geffroy, I. Denghien, N. Souedet, and Y. Cointepas. BrainVISA: **An extensible software environment for sharing multimodal neuroimaging data and processing tools**, In *Proc. 15th HBM*, 2009. |riviere09|

Rivière, D. Geffroy, I. Denghien, N. Souedet, and Y. Cointepas. BrainVISA: **An extensible software environment for sharing multimodal neuroimaging data and processing tools**, In *Proc. 15th HBM*, 2009. |riviere09|

Rivière, D. Geffroy, I. Denghien, N. Souedet, and Y. Cointepas. BrainVISA: 

**An extensible software environment for sharing multimodal neuroimaging data and processing tools**

An extensible software environment for sharing multimodal neuroimaging data and processing tools

.. |cointepas10| image:: images/pdf.png
    :target: https://brainvisa.info/download/papers/Cointepas-HBM10_poster.pdf

Y. Cointepas, D. Geffroy, N. Souedet, I. Denghien, and D. Rivière: **The BrainVISA project: a shared software development infrastructure for biomedical imaging research**, In *Proc. 16th HBM*, 2010. |cointepas10|

Cointepas, D. Geffroy, N. Souedet, I. Denghien, and D. Rivière: **The BrainVISA project: a shared software development infrastructure for biomedical imaging research**, In *Proc. 16th HBM*, 2010. |cointepas10|

Cointepas, D. Geffroy, N. Souedet, I. Denghien, and D. Rivière: 

**The BrainVISA project: a shared software development infrastructure for biomedical imaging research**

The BrainVISA project: a shared software development infrastructure for biomedical imaging research

.. |geffroy11| image:: images/pdf.png
    :target: http://static.lnao.fr/papers/brainvisa_python_neuroscience.pdf

D. Geffroy, D. Rivière, I. Denghien, N. Souedet, S. Laguitton, and Y. Cointepas: **BrainVISA: a complete software platform for neuroimaging**, In *Python in Neuroscience workshop*, Paris, Aug. 2011.

Geffroy, D. Rivière, I. Denghien, N. Souedet, S. Laguitton, and Y. Cointepas: **BrainVISA: a complete software platform for neuroimaging**, In *Python in Neuroscience workshop*, Paris, Aug. 2011.

Geffroy, D. Rivière, I. Denghien, N. Souedet, S. Laguitton, and Y. Cointepas: 

.. |laguitton11| image:: images/pdf.png
    :target: https://brainvisa.info/download/papers/soma-workflow/poster_HBM_2011_somaworkflow.pdf

S. Laguitton, D. Rivière, D. Geffroy, N. Souedet, and Y. Cointepas: **Soma-Workflow: open source software for easy access to parallel computing resources**, In *Proc. 17th HBM*, 2011. |laguitton11|

Laguitton, D. Rivière, D. Geffroy, N. Souedet, and Y. Cointepas: **Soma-Workflow: open source software for easy access to parallel computing resources**, In *Proc. 17th HBM*, 2011. |laguitton11|

Laguitton, D. Rivière, D. Geffroy, N. Souedet, and Y. Cointepas: 

**Soma-Workflow: open source software for easy access to parallel computing resources**

Soma-Workflow: open source software for easy access to parallel computing resources

.. |laguitton11b| image:: images/pdf.png
    :target: https://brainvisa.info/download/papers/soma-workflow/MICCAI_2011_soma_workflow.pdf

S. Laguitton, D. Rivière, T. Vincent, C. Fischer, D. Geffroy, N. Souedet, I. Denghien, and Y. Cointepas: **Soma-workflow: a unified and simple interface to parallel computing resources**, In *MICCAI Workshop on High Performance and Distributed Computing for Medical Imaging*, Toronto, Sep. 2011. |laguitton11b|

Laguitton, D. Rivière, T. Vincent, C. Fischer, D. Geffroy, N. Souedet, I. Denghien, and Y. Cointepas: **Soma-workflow: a unified and simple interface to parallel computing resources**, In *MICCAI Workshop on High Performance and Distributed Computing for Medical Imaging*, Toronto, Sep. 2011. |laguitton11b|

Laguitton, D. Rivière, T. Vincent, C. Fischer, D. Geffroy, N. Souedet, I. Denghien, and Y. Cointepas: 

**Soma-workflow: a unified and simple interface to parallel computing resources**

Soma-workflow: a unified and simple interface to parallel computing resources

*MICCAI Workshop on High Performance and Distributed Computing for Medical Imaging*

MICCAI Workshop on High Performance and Distributed Computing for Medical Imaging

.. |laguitton11c| image:: images/pdf.png
    :target: https://brainvisa.info/download/papers/soma-workflow/pythonneuro_2011_soma_workflow.pdf

S. Laguitton, D. Rivière, T. Vincent, C. Fischer, D. Geffroy, N. Souedet, I. Denghien, and Y. Cointepas: **Soma-workflow: a unified and simple interface to parallel computing resources**, In *Python in Neuroscience workshop*, Paris, Aug. 2011. |laguitton11c|

Laguitton, D. Rivière, T. Vincent, C. Fischer, D. Geffroy, N. Souedet, I. Denghien, and Y. Cointepas: **Soma-workflow: a unified and simple interface to parallel computing resources**, In *Python in Neuroscience workshop*, Paris, Aug. 2011. |laguitton11c|

.. |riviere11| image:: images/pdf.png
    :target: https://brainvisa.info/download/papers/anatomist_euroscipy_neuro.pdf

D. Rivière, D. Geffroy, I. Denghien, N. Souedet, and Y. Cointepas: **Anatomist: a python framework for interactive 3D visualization of neuroimaging data**, In *Python in Neuroscience workshop*, 2011. |riviere11| :anatomist:`slides <pyanatomist_overview.pdf>`

Rivière, D. Geffroy, I. Denghien, N. Souedet, and Y. Cointepas: **Anatomist: a python framework for interactive 3D visualization of neuroimaging data**, In *Python in Neuroscience workshop*, 2011. |riviere11| :anatomist:`slides <pyanatomist_overview.pdf>`

Rivière, D. Geffroy, I. Denghien, N. Souedet, and Y. Cointepas: 

**Anatomist: a python framework for interactive 3D visualization of neuroimaging data**

Anatomist: a python framework for interactive 3D visualization of neuroimaging data

:doc:`morphologist`, `Cortical Surface <http://www.meca-brain.org/softwares/>`_, :doc:`brainrat`, etc.

Search and ask questions on https://github.com/brainvisa/brainvisa.github.io/discussions. You will need a GitHub account to post messages.

The former `BrainVisa forum <../forum/>`_ has been stopped because it was not working well. It is still available in read-only mode to search questions / answers which have already been asked. New questions should be posted on the above gitHub disucssions area.

 has been stopped because it was not working well. It is still available in read-only mode to search questions / answers which have already been asked. New questions should be posted on the above gitHub disucssions area.

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SnapBase allows to take snapshots of various neuroimaging data, for a set of subjects or entire databases. It may also make "poster" maps with all snapshots in a large picture. It is thus a convenient way to perform fast quality checks on the results of large datasets processings.

SnapBase allows to take snapshots of various neuroimaging data, for a set of subjects or entire databases. It may also make “poster” maps with all snapshots in a large picture. It is thus a convenient way to perform fast quality checks on the results of large datasets processings.

It can run independently of BrainVISA, or use the BrainVISA databasing facilities to select data.

SnapBase is designed as a modular tool: custom additional snapshot types may be added.

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Analysis of the laminar structure of the cortex in high resolution MRI

For now it is a development library and tools, available on a public sources repository:

See also the :hr_cortex:`development docs <doxygen/index.html>`.

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A segmentation toolbox dedicated to primate brain images is developed in MirCen, BioPicsel team. It is making use of some steps of the :doc:`morphologist` pipeline, but is based on a probabilistic framework. It is designed to process macaque brains with T2 contrasts.

A segmentation toolbox dedicated to primate brain images is developed in MirCen, BioPicsel team. It is making use of some steps of the 

 pipeline, but is based on a probabilistic framework. It is designed to process macaque brains with T2 contrasts.

:axon:`The toolbox documentation can be seen here <en/processes/categories/primatologist/category_documentation.html>`.