
  Section of Biomedical Image Analysis
  Department of Radiology
  University of Pennsylvania
  3600 Market Street, Suite 380
  Philadelphia, PA 19104

  Web:   https://www.rad.upenn.edu/sbia/
  Email: sbia-software at uphs.upenn.edu

  Copyright (c) 2012, University of Pennsylvania. All rights reserved.
  See http://www.rad.upenn.edu/sbia/software/license.html or COPYING file.



INTRODUCTION
============

  This document contains the build and installation instructions.

  For general build and installation instructions which apply to any software
  developed on top of the SBIA Build system And Software Implementation Standard
  (BASIS) [1], please refer to the INSTALL-basis document which can be either found
  in the doc/ directory of your BASIS installation or online at [2].



OBTAINING A COPY OF THE SOFTWARE
================================

  Please see corresponding section in the INSTALL-basis document [2].



INSTALLING A BINARY DISTRIBUTION PACKAGE
========================================

  Please see corresponding section in the INSTALL-basis document [2].



RUNTIME REQUIREMENTS
====================

  This software has no runtime dependencies.



BUILDING THE SOFTWARE FROM SOURCES
==================================

  In the following, only the additional build dependencies and CMake settings
  available to configure this software package are summarized. For a list of
  general build dependencies and step-by-step instructions on how to use CMake
  and GNU Make to build and install the software, please refer to the
  corresponding section in the INSTALL-basis document [2].


  Build Dependencies
  ------------------

  - BASIS 1.2 or greater

    Web Site: http://www.rad.upenn.edu/sbia/software/doxygen/basis/1.2/html/
    Download: http://www.rad.upenn.edu/sbia/software/distributions/basis-1.2.0-source.tar.gz

    This project is based on BASIS, a meta-project developed at SBIA to
    standardize and simplify the software development.

  - ATLAS 3.8.3 or greater
 
    Web Site: http://math-atlas.sourceforge.net/
    Download: https://sourceforge.net/projects/math-atlas/files/Stable/
    Ubuntu:   libatlas-dev

  - Boost 1.33 or greater

    Web Site: http://www.boost.org/
    Download: http://www.boost.org/users/download/
    Ubuntu:   libboost-dev

  - boost-numeric-bindings 20081116 or later

    Web Site: http://mathema.tician.de/software/boost-numeric-bindings
    Download: http://mathema.tician.de/dl/software/boost-numeric-bindings

    In particular, the ATLAS bindings are used by this software.

  - nifticlib 1.1 or greater

    Web Site: http://niftilib.sourceforge.net/
    Download: http://sourceforge.net/projects/niftilib/files/nifticlib/
    Ubuntu:   libnifti1-dev or nifticlib

  - OpenCV 1.0 or 1.1pre1

    Web Site: http://opencv.willowgarage.com/wiki/
    Download: https://sourceforge.net/projects/opencvlibrary/files/
    Ubuntu:   libcv-dev, libcvaux-dev (hardy)

    Note that with OpenCV 2 (we tried versions 2.0.0, 2.2.0 and 2.3.1),
    the runtime of ODVBA suffers quite some. It is strongly recommended to
    build this software with OpenCV 1.0.0 or OpenCV 1.1pre1.

    In future versions of ODVBA it may need to be investigated how this
    performance issue can be resolved. The cvEigenVV() C function of OpenCV 2
    used by the Non-negative Discriminative Projection (NDP) seems to be the
    bottleneck. It would be worthwhile to give the C++ equivalent a shot.
    Another solution might be the use of cvSVD() or its C++ counterpart.

  - Open MPI 1.3.3 or greater (optional)

    Web Site: http://www.open-mpi.org/
    Download: http://www.open-mpi.org/software/ompi/v1.4/
    Ubuntu:   mpi-default-dev

    If an Open MPI library is found on your system, the odvba-mpi executable
    is build next to the serial odvba executable. The odvba-mpi executable
    is suitable for execution on either one machine with multiple cores or,
    in particular, on a cluster with multiple compute nodes. A subset of the
    total number of permutation tests is then performed by separate Open MPI
    processes. The results are assembled in the end by the main process to
    write the final results.


  CMake Options
  -------------

  (no additional CMake options considered by this package)


  Advanced CMake Options
  ----------------------

  (no additional advanced CMake options considered by this package)



REFERENCES
==========

  [1] http://sourceforge.net/projects/sbia-basis/
  [2] Visit http://www.rad.upenn.edu/sbia/software/installation.html or see
      the INSTALL-basis document in the doc/ directory of the BASIS installation.
