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.