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.
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General help and project information:
http://sourceforge.net/projects/sivic/
http://sourceforge.net/apps/trac/sivic/
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The Doxygen C++ API for SIVIC is published on Sourceforge:
http://sivic.sourceforge.net/libsvk/html/index.html
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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.