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Welcome to SABRE's documentation!
=================================
SABRE (Semi-Automatic Brain Region Extraction) is a comprehensive semi-automatic pipeline that yields an individualized volumetric profile of regionalized tissue and lesion classes. This pipeline was developed by `SABRE BrainLab <http://sabre.brainlab.ca/index.html>`_ within the L.C. Campbell Cognitive Neurology Research Unit at `Sunnybrook Research Institute <http://sunnybrook.ca/research/>`_ in Toronto, Canada.

Starting with version 2.0, SABRE is implemented using the open-source `Nipype <http://nipy.sourceforge.net/nipype/>`_ workflow engine for neuroimaging software. The SABRE pipeline integrates original software developed by SABRE BrainLab with tools from `FSL <http://www.fmrib.ox.ac.uk/fsl/>`_, `ANTs <http://stnava.github.io/ANTs/>`_ and `AIR <http://bishopw.loni.ucla.edu/air5/overview.html>`_.

The source code of SABRE is available from the Sunnybrook Brain Imaging Processing Software `repository on GitHub <https://github.com/sbips>`_.

To receive instructions on setting up the software, please `fill in the linked form <https://docs.google.com/forms/d/1dEhMxf2th90I4iTocmxKY6m4vvz6Dp7QEVEzXVvqH54/viewform>`_.

Contents:

.. toctree::
   :maxdepth: 2

   processing/index
   pipeline/index
  
Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`