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SIVIC is an open-source, standards-based software framework and application suite for processing and visualizing DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. The SIVIC code repository lives on github but our user portal is on sourceforge.

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SIVIC

This is an early stage relese of SIVIC. All comments/questions are welcome. This is a community project and participation is encouraged. Please see the following links for further information.

  1. General help and project information:

    http://sourceforge.net/projects/sivic/

    http://sourceforge.net/apps/trac/sivic/

  2. The Doxygen C++ API for SIVIC is published on Sourceforge:

    http://sivic.sourceforge.net/libsvk/html/index.html

  3. Mail List

    https://lists.sourceforge.net/lists/listinfo/sivic-users

NOTES FOR WINDOWS USERS: * To run sivic simply double click on sivic_windows/bin/sivic.bat, or run from the msdos prompt. * This version of sivic should run on Windows Vista, Windows 7, and Windows 2003 Server. * Some features are disabled in the Windows version (using the "exam" button and the quantification demo). These features should be available soon. * Command line tools are not yet available, but also should be soon. * Please contact us via the sourceforge site above if you have any problems.

HOW TO BUILD SIVIC

BUILDING DEPENDENCIES

This was Built using CentOS 7.9 ( GCC 4.8.5 / GLIBC 2.17). Build is forward compatible with RHEL8 and RHEL9. Needs to build on a redhat 7 sever .

1.Build and install TCL and TK packages

https://sourceforge.net/projects/tcl/files/Tcl/8.5.19/tcl8.5.19-src.tar.gz/download
https://sourceforge.net/projects/tcl/files/Tcl/8.5.19/tk8.5.19-src.tar.gz/download

  • Open up terminal and CD into TCL
  • cd into unix director
  • ./configure --prefix=/usr/local/sivic/build/deps/tcl8.5.19 --enable-shared
  • Make -j
  • Make install
  • Open up terminal and CD into TK
  • cd into unix directory
  • ./configure --with-x --prefix=/usr/local/sivic/build/deps/tk8.5.19 --with-tcl=/usr/local/sivic/build/deps/tcl8.5.19/lib --enable-shared
  • make -j
  • make install

2.Build and install DCMTK 3.6.7

https://dicom.offis.de/download/dcmtk/dcmtk367/dcmtk-3.6.7.tar.gz

  • Open up terminal and CD into DCMTK
  • cmake .
  • ccmake .
    • BUILD_SHARED_LIBS=ON
    • CMAKE_INSTALL_PREFIX=/usr/local/sivic/build/deps/dcmtk-3.6.7
  • make -j
  • make install

3.Build and install ITK 4.4.1

https://github.com/InsightSoftwareConsortium/ITK/archive/refs/tags/v4.4.1.tar.gz

  • Open up terminal and CD into ITK
  • mkdir ITK-Sandbox
  • cd ITK-sandbox
  • git clone https://github.com/InsightSoftwareConsortium/ITK.git
  • mkdir ITK-build
  • cd ITK-build
  • cmake .
  • ccmake .
    • BUILD_EXAMPLES=OFF
    • BUILD_SHARED_LIBS=ON
    • BUILD_TESTING=OFF
    • CMAKE_INSTALL_PREFIX=/usr/local/sivic/build/deps/ITK-4.4.1
  • Make
  • Make install

4.Build and install clapack 3.2.1

https://www.netlib.org/clapack/clapack-3.2.1-CMAKE.tgz

  • Open up terminal and cd into clapack
  • cmake .
  • ccmake . - BUILD_TESTING=OFF - CMAKE_INSTALL_PREFIX=/usr/local/sivic/build/deps/clapack-3.2.1 - USE_BLAS_WRAP=ON
  • Make
  • Make install
  • bash-4.2$ cd /usr/local/sivic/build/deps/clapack-3.2.1/lib
  • bash-4.2$ ln -s liblapack.a libclapack.a
  • bash-4.2$ ln -s libblas.a libcblas.a

5.Build and install VTK 6.3.0

https://gitlab.kitware.com/vtk/vtk/-/archive/v6.3.0/vtk-v6.3.0.tar.gz

  • Open up terminal and cd into VTK]
  • cmake .
  • ccmake ..
    • BUILD_SHARED_LIBS=ON
    • BUILD_TESTING=OFF
    • CMAKE_INSTALL_PREFIX=/usr/local/sivic/build/deps/VTK-6.3.0
    • VTK_Group_Tk=ON
    • VTK_USE_TK=ON
    • VTK_TCL_TK_STATIC=ON
    • Module_vtkWrappingTcl=ON
    • Module_vtkTclTk=ON
    • TCL_LIBRARY=/usr/local/sivic/build/deps/tcl8.5.19/lib/libtcl8.5.so
    • TCL_TCLSH=/usr/local/sivic/build/deps/tcl8.5.19/bin/tclsh8.5
    • TK_INCLUDE_PATH=/usr/local/sivic/build/deps/tk8.5.19/include
    • TK_LIBRARY=/usr/local/sivic/build/deps/tk8.5.19/lib/libtk8.5.so
  • Make
  • Make install

6.set environment variables for DCMTK_DIR and VTK_DIR

  • export DCMTK_DIR=/usr/local/sivic/build/deps/dcmtk-3.6.7
  • export VTK_DIR=/usr/local/sivic/build/deps/VTK-6.3.0

7.Build and Install KWWidgets

  • open up and terminal
  • CD into KWWidgets
  • cmake .
  • cmake ..
    • BUILD_TESTING = OFF
    • CMAKE_INSTALL_PREFIX=/usr/local/sivic/build/deps/KWWidgets
    • VTK_DIR=/usr/local/sivic/build/deps/VTK-6.3.0/lib/cmake/vtk-6.3
    • TCL_INCLUDE_PATH=/usr/local/sivic/build/deps/tcl8.5.19/include
    • TCL_LIBRARY=/usr/local/sivic/build/deps/tcl8.5.19/lib/libtcl8.5.so
    • TCL_TCLSH=/usr/local/sivic/build/deps/tcl8.5.19/bin/tclsh8.5
    • TK_INCLUDE_PATH=/usr/local/sivic/build/deps/tk8.5.19/include
    • TK_LIBRARY=/usr/local/sivic/build/deps/tk8.5.19/lib/libtk8.5.so
  • make
  • make install

8.Build and install openssl

https://github.com/openssl/openssl/archive/refs/tags/openssl-3.0.7.tar.gz

  • ../configure --prefix=/usr/local/sivic/build/deps/openssl-openssl-3.0.7
  • make -j 4
  • make install
  • cd /usr/local/sivic/build/deps/openssl-openssl-3.0.7
  • ln -s lib64 lib

BUILDING SIVIC

  • In redhat 7 server, open up terminal,
  • mkdir sivic-rh9
  • Git clone https://github.com/SIVICLab/sivic.git
  • mkdir lnx68
  • cd lnx68
  • ccmake ..
  • press [c] to configure
    • BUILD_APPS=ON
    • BUILD_CREATE_RAW=ON
    • BUILD_CLAPACK=ON
    • BUILD_ITK = ON
    • BUILD_LIBRARY = ON
    • BUILD_VIZ_LIBRARY = ON
    • CLAPACK_DIR=/usr/local/sivic/build/deps/clapack-3.2.1/lib
    • CMAKE_INSTALL_PREFIX=/usr/local/sivic/sivic
    • DCMTK_DIR=/usr/local/sivic/build/deps/dcmtk-3.6.7
    • ITK_DIR=/sivic/build/deps/ITK-4.4.1/lib/cmake/ITK-4.4
    • KWWidgets DIR =/usr/local/sivic/build/deps/KWWidgets/lib/KWWidgets
    • VTK_DIR=/usr/local/sivic/build/deps/VTK-6.3.0/lib/cmake/vtk-6.3
    • OPENSSL_DIR=/usr/local/sivic/build/deps/openssl-openssl-3.0.7
    • UCSF_INTERNAL=ON
  • Make
  • Make install

Citations

SIVIC. Available online at: https://sourceforge.net/p/sivic/sivicwiki/Home/ DOI: 10.5281/zenodo.4777197

Crane, Jason C., Marram P. Olson, and Sarah J. Nelson. “SIVIC: Open-Source, Standards-Based Software for DICOM MR Spectroscopy Workflows.” International Journal of Biomedical Imaging 2013 (July 18, 2013): e169526. https://doi.org/10.1155/2013/169526.

About

SIVIC is an open-source, standards-based software framework and application suite for processing and visualizing DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. The SIVIC code repository lives on github but our user portal is on sourceforge.

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