Gadgetron prerequisites

These steps are required, if one wants to use the CS LAB C++ code or any Gadgetron code.

Linux

mkdir build cd build cmake ../ make 

Windows

According to the instructions in here, this following sequential procedure worked out for us.

Assuming you are going to install Gadgetron to "D:\ProgramFiles\Gadgetron":

1.) Install Visual Studio 2010 with Service Pack 1

2.) CUDA (https://developer.nvidia.com/cuda-downloads)

– install cuda_5.5.20_winvista_win7_win8_general_64.exe

3.) CULA (http://www.culatools.com/downloads/dense/)

– install cula_dense_free_R16a-windows.exe

– add installation path to environment variable PATH (Control Panel → System → Advanced system setting → Environment Variables):

e.g. C:\Program\CULA\R16 and C:\Program Files\CULA\R16\bin64

4.) FFTW (http://www.fftw.org/install/windows.html)

– copy binaries from fftw-3.3.4-dll64.zip to D:\ProgramFiles\Gadgetron\Libraries\FFTW3

– open Visual Studio x64 Win64 Command Prompt and execute:

D:\ProgramFiles\Gadgetron\Libraries\FFTW3>lib /machine:x64 /def:libfftw3f−3.def

D:\ProgramFiles\Gadgetron\Libraries\FFTW3>lib /machine:x64 /def:libfftw3−3.def

D:\ProgramFiles\Gadgetron\Libraries\FFTW3>lib /machine:x64 /def:libfftw3l−3.def

– the *.lib files are created

– add D:\ProgramFiles\Gadgetron\Libraries\FFTW3 to PATH environment variable

– alternatively, follow the instructions on http://www.fftw.org/install/windows.html for compiling the FFTW library by yourself

5.) ACE (http://download.dre.vanderbilt.edu/)

– unzip ACE-6.2.0.zip to D:\ProgramFiles\Gadgetron\Libraries\ACE-6.2.0

– add file config.h to ..\ACE_wrappers\ace\

– open config.h and insert:

//We are on Windows

#include "ace/config − win32.h"

//This ensured that INLINE settings

//do not vary between Debug and Release modes

#define ACE_NO_INLINE

– open VS 2010 solution ACE_wrappers_vc10.sln in D:\ProgramFiles\Gadgetron\Libraries\ACE-6.2.0\ACE_wrappers\

– set build type to Release/x64 and start build

– add D:\ProgramFiles\Gadgetron\Libraries\ACE-6.2.0\ACE_wrappers\lib to PATH

6.) Python (optional - http://www.python.org/)

– install python-2.7.7.amd64.msi in C:\Python27 and add it to PATH

– install numpy-MKL-1.8.1.win-amd64-py2.7.exe, scipy-0.14.0.win-amd64-py2.7.exe and libxml2-python-2.9.1.win-amd64-py2.7.exe

7.) ACML (optional - http://developer.amd.com/tools-and-sdks/cpu-development/amd-core-math-library-acml/acml-archive-downloads/)

– install acml5.3.0-win64.exe

– add D:\ProgramFiles\Gadgetron\Libraries\acml5.3.0\win64_mp\lib and D:\ProgramFiles\Gadgetron\Libraries\acml5.3.0\win64\lib to PATH

8.) Boost Pro (http://www.boost.org/)

– unzip boost_1_55_0.zip to D:\ProgramFiles\Gadgetron\Libraries\boost\boost_1_55_0

– open Visual Studio x64 Win64 Command Prompt and execute:

cd D:\ProgramFiles\Gadgetron\Libraries\boost\boost_1_55_0

bootstrap

b2 address − model=64 −− build − type=complete stage

– add D:\ProgramFiles\Gadgetron\Libraries\boost\boost_1_55_0\stage\lib to PATH

9.) git (optional - http://code.google.com/p/msysgit)

– install Git-1.9.4-preview20140611.exe with git bash only and checkout Windows LF and commit Unix LF option

10.) CMake (http://www.cmake.org/cmake/resources/software.html)

– install cmake-2.8.12.2-win32-x86.exe

11.) HDF5 (http://www.hdfgroup.org/HDF5)

– install hdfview_install_win64.exe

– unzip hdf5-1.8.12-win64-vs10shared.zip and install HDF5-1.8.12-win64.exe

– add C:\Program Files\HDF Group\HDF5\1.8.12\bin to PATH

12.) CodeSynthesis XSD (http://www.codesynthesis.com/download/xsd/3.3/windows/i686/xsd-3.3.msi)

– install xsd-3.3.msi

– add C:\Program Files (x86)\CodeSynthesis XSD 3.3\bin\ and C:\Program Files (x86)\CodeSynthesis XSD 3.3\bin64\ to PATH

13.) ISMRMRD (http://ismrmrd.github.io/)

– optional (required for MATLAB Gadget or utilize XML parser): install JAVA (take MATLAB Jave version) jdk-7u11-windows-x64.exe

– download and copy source code to D:\ProgramFiles\Gadgetron\Libraries\ismrmrd-code

– create directory build in D:\ProgramFiles\Gadgetron\Libraries\ismrmrd-code

– open CMake and set source code to: D:\ProgramFiles\Gadgetron\Libraries\ismrmrd-code and build to: D:\ProgramFiles\Gadgetron\Libraries\ismrmrd-code\build

– hit configure

– set paths to: Boost, FFTW3, HDF5, JAVA, XERXESC, XSD in cmake file

BOOST_ROOT=D:/ProgramFiles/Gadgetron/Libraries/boost/boost_1_55_0 XSD_EXECUTABLE=C:/Program Files (x86)/CodeSynthesis XSD 3.3/bin/xsd.exe XSD_INCLUDE_DIR=C:/Program Files (x86)/CodeSynthesis XSD 3.3/include HDF5_DIR=C:/Program Files/HDF Group/HDF5/1.8.12/cmake/hdf5 HDF5_CXX_LIBRARY=C:/Program Files/HDF Group/HDF5/1.8.12/lib/hdf5_cppdll.lib HDF5_C_LIBRARY=C:/Program Files/HDF Group/HDF5/1.8.12/lib/hdf5dll.lib HDF5_C_INCLUDE_DIR=C:/Program Files/HDF Group/HDF5/1.8.12/include HDF5_CXX_INCLUDE_DIR=C:/Program Files/HDF Group/HDF5/1.8.12/include FFTW3F_LIBRARY=D:/ProgramFiles/Gadgetron/Libraries/FFTW3/libfftw3f-3.lib FFTW3_INCLUDE_DIR=D:/ProgramFiles/Gadgetron/Libraries/FFTW3 XERCESC_INCLUDE_DIR=C:/Program Files (x86)/CodeSynthesis XS D3.3/include/xercesc XERCESC_LIBRARIES=C:/Program Files (x86)/CodeSynthesis XSD 3.3/lib64/vc-10.0/xerces-c_3.lib

and change the install path to: D:\ProgramFiles\Gadgetron\Libraries\install

– hit configure

– if no error occurs, hit generate (in case of an error deal with the dependencies until all errors are gone)

– overwrite the file ismrmrd.cxx with the file from the linux solution

– open the Visual Studio solution ISMRMRD.sln and change the preprocessor definition in the project jismrmrd from jismrmrd_EXPORTS to ismrmrd_EXPORTS

– compile and install (build project INSTALL)

– if an error occurs,

∗ check the HDF5 libraries in Linker → Input and set the correct name in all projects

∗ check the entry in C/C++ → General → Additional Include Directories (..\HDFGroup\HDF5\1.8.12\include )

– add D:\ProgramFiles\Gadgetron\Libraries\install\ismrmrd\bin and D:\ProgramFiles\Gadgetron\Libraries\install\ismrmrd\lib to PATH

14.) Google Test (optional - https://code.google.com/p/googletest/downloads/detail?name=gtest-1.7.0.zip)

– unzip gtest-1.7.0.zip to D:\ProgramFiles\Gadgetron\Libraries\gtest-1.7.0

– create directory D:\ProgramFiles\Gadgetron\Libraries\gtest-1.7.0\vc10

– open CMake and set source code to: D:\ProgramFiles\Gadgetron\Libraries\gtest-1.7.0 and build to: D:\ProgramFiles\Gadgetron\Libraries\gtest-1.7.0\vc10

– hit configure and set BUILD_SHARED_LIBS, gtest_force_shared_crt and gtet_disable_pthreads

– hit generate

– open the Visual Studio solution gtest.sln and compile in debug and release version

15.) Armadillo C++ (http://arma.sourceforge.net/download.html)

– unzip armadillo-4.000.2.tar.gz to D:\ProgramFiles\Gadgetron\Libraries\armadillo-4.000.2

– create directory vc10 in ..\Libraries\armadillo-4.000.2\

– open CMake and set source code to: D:\ProgramFiles\Gadgetron\Libraries\armadillo-4.000.2 and build to: D:\ProgramFiles\Gadgetron\Libraries\armadillo-4.000.2\vc10

– open the file D:\ProgramFiles\Gadgetron\Libraries\armadillo-4.000.2\include\armadillo_bits\config.hpp

– change the following entries in the file to:

#define ARMA_USE_LAPACK

#define ARMA_USE_BLAS

#define ARMA_BLAS_CAPITALS

#define ARMA_BLAS_UNDERSCORE

#define ARMA_BLAS_LONG_LONG

– hit configure and generate (in CMake)

– open the Visual Studio solution armadillo.sln in ..\vc10

– compile and install (build project INSTALL)

– uncomment #define ARMA_BLAS_LONG_LONG in the config.hpp again

– add D:\ProgramFiles\Gadgetron\Libraries\armadillo-4.000.2\include\lib to PATH

16.) xsltproc (http://xmlsoft.org/sources/win32)

– download and copy the directory xslt to D:\ProgramFiles\Gadgetron\Libraries\xslt

17.) install Gadgetron