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ismrmrd / philips_to_ismrmrd

Philips to ISMRMRD converter
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philips_to_ismrmrd

A tool for converting Philips raw MR data into ISMRMRD format.

Dependencies

Build

Mac OS X

  1. Install dependencies

    • Example commands to acquire dependencies and build ismrmrd using brew tested on Mac OS X 10.10.5 Yosemite, XCode version 2339

      • If you already have brew, you should make sure it is up-to-date
      brew update
      • Otherwise, install brew
      ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
      • Then install ismrmrd dependencies
      brew install wget cmake doxygen boost fftw
      • If you have the anaconda distribution of python, you should already have hdf5, but you should make sure everything is up-to-date
      conda update
      • Otherise, let brew install hdf5
      brew tap homebrew/science
brew install homebrew/science/hdf5
      • Download, compile and install ismrmrd
      git clone https://github.com/ismrmrd/ismrmrd
cd ismrmrd
mkdir build
cd build
cmake ..
make install

  2. Get the code: 

    git clone https://github.com/ismrmrd/philips_to_ismrmrd

  3. Generate build files, compile, and install:

    cd philips_to_ismrmrd
mkdir build
cd build
cmake ..
make install

    • If cmake complains about missing libxml2 and/or libxslt, you can use brew to fix it

      brew install libxml2
brew link --force libxml2

    • and/or

      brew install libxslt
brew link --force libxslt

    • then try again

      cmake ..
make install

Linux

  1. Install dependencies

    • Example commands to acquire dependencies and build ismrmrd using apt-get tested on Ubuntu 14.04.3 LTS

      sudo apt-get update
sudo apt-get install build-essential git cmake cmake-qt-gui doxygen libboost-all-dev fftw-dev libhdf5-serial-dev hdf5-tools
git clone https://github.com/ismrmrd/ismrmrd
cd ismrmrd
mkdir build
cd build
cmake ..
make
sudo make install
sudo ldconfig

    • Example commands to acquire philips_to_ismrmrd dependencies libxml and libxslt using apt-get tested on Ubuntu 14.04.3 LTS

      sudo apt-get install libxml2-dev libxslt1-dev

  2. Get the code: 

    git clone https://github.com/ismrmrd/philips_to_ismrmrd

  3. Generate build files, compile, and install:

    cd philips_to_ismrmrd
mkdir build
cd build
cmake ..
sudo make install

Windows 7 (tested with Visual Studio Pro 2013)

  1. Compile and install 32-bit version (not 64-bit version) of ismrmrd following steps inspired by instructions found here

    • Add C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin to system path environment variable

    • Copy 32-bit FFTW3 binaries to C:\Libraries\FFTW3

    • Create FFTW3 .lib files on the command line with:

      c:\Libraries\FFTW3>lib /machine:x86 /def:libfftw3f-3.def
c:\Libraries\FFTW3>lib /machine:x86 /def:libfftw3-3.def
c:\Libraries\FFTW3>lib /machine:x86 /def:libfftw3l-3.def

    • Add C:\Libraries\FFTW3 to the system path environment variable

    • Install boost_1_55_0-msvc-12.0-32.exe available here to location C:\Libraries\boost_1_55_0

    • Install hdf5-1.8.15-win32-vs2013-shared.zip available here to location C:\local\HDF_Group\HDF5\1.8.15\

    • Install CMake available here and add to system path environment variable

    • Get the ismrmrd code using git clone https://github.com/ismrmrd/ismrmrd or download zip and save to a parent folder located at C:\Libraries\ismrmrd

    • Create folder C:\Libraries\ismrmrd\build

    • Set the following system environment variables (forward slashes, no quotes)

      FFTW3_ROOT_DIR = C:/Libraries/FFTW3
BOOST_ROOT = C:/Libraries/boost_1_55_0
BOOST_LIBRARYDIR = C:/Libraries/boost_1_55_0/lib32-msvc-12.0
HDF5_DIR = C:/local/HDF_Group/HDF5/1.8.15/cmake

    • Run CMake GUI with following entries

      Where is the source code: C:/Libraries/ismrmrd
Where to build the binaries: C:/Libraries/ismrmrd/build

    • Click CMake Configure button and select options

      Generator: Visual Studio 12 2013
Use default native compilers

    • Open C:\Libraries\ismrmrd\build\ISMRMRD.sln created by CMake

    • Change from Debug to Release

    • In Solution Explorer window, right-click ismrmrd and select properties -> C/C++ -> General -> Additional Include Directories and insert C:\local\HDF_Group\HDF5\1.8.15\include

    • Using a text editor outside Visual Studio, replace all occurrences of bin\hdf5.dll with lib\hdf5.lib in ./ismrmrd.vcxproj, ./examples/c/ismrmrd_c_example.vcxproj, ./utilities/ismrmrd_generate_cartesian_shepp_logan.vcxproj, ./utilities/ismrmrd_info.vcxproj, ./utilities/ismrmrd_read_timing_test.vcxproj, ./utilities/ismrmrd_recon_cartesian_2d.vcxproj

    • Return to Visual Studio, select "Reload All" to load altered .vcxproj files

    • Select BUILD -> Build Solution

    • Install NSIS Windows installer creator available here

    • Create a README.html file for packaging

      copy C:\Libraries\ismrmrd\README.md C:\Libraries\ismrmrd\README.html

    • Edit C:\Libraries\ismrmrd\build\CPackConfig.cmake and replace all occurrences of "C:/Program Files (x86)/ISMRMRD" with "/ISMRMRD"

    • Create installer package from the command line

    cd C:\Libraries\ismrmrd\build
cpack

    • Run installer created at location C:/Libraries/ismrmrd/build/ismrmrd-1.3.2.exe and select add ISMRMRD to path for all users and install to parent folder C:\local\ismrmrd

    • Add C:\local\ismrmrd\ISMRMRD\lib to the system path environment variable

  2. Download philips_to_ismrmrd dependencies libxml and libxslt

    • Download iconv-1.9.2.win32.zip, libxml2-2.6.30.win32.zip, libxslt-1.1.26.win32.zip and zlib-1.2.5.win32.zip available here and install to C:\Libraries\iconv-1.9.2.win32, C:\Libraries\libxml2-2.6.30.win32, C:\Libraries\libxslt-1.1.26.win32 and C:\Libraries\zlib-1.2.5 respectively
    • Add C:\Libraries\iconv-1.9.2.win32\bin;C:\Libraries\libxml2-2.6.30.win32\bin;C:\Libraries\libxslt-1.1.26.win32\bin;C:\Libraries\zlib-1.2.5\bin to the system path environment variable

  3. Get the philips_to_ismrmrd code using git clone https://github.com/ismrmrd/philips_to_ismrmrd or download zip with parent folder located at C:\Libraries\philips_to_ismrmrd

  4. Prepare to compile from the command-line

    cd "c:\Program Files (x86)\Microsoft Visual Studio 12.0\VC"
vcvarsall x86

  5. Compile philips_to_ismrmrd.exe

    cd c:\Libraries\philips_to_ismrmrd
cl main.cpp pugixml.cpp /EHa /Fephilips_to_ismrmrd.exe /GS /TP /W3 /Zc:wchar_t- /Gm- /O2 /Ob2 /D "WIN32" /D "_WINDOWS" /D "NDEBUG" /D "_WIN32" /D "UNICODE" /D "_UNICODE" /D "_CRT_SECURE_NO_WARNINGS" /D "__func__=__FUNCTION__" /WX- /Zc:forScope /Gd /MD /I"C:/Libraries/iconv-1.9.2.win32/include/" /I"C:/Libraries/libxml2-2.6.30.win32/include/" /I"C:/Libraries/boost_1_55_0/" /I"C:/Libraries/libxml2-2.6.30.win32/include/" /I"C:/Libraries/libxslt-1.1.26.win32/include/" /I"C:/local/ismrmrd/ISMRMRD/include/" /link /libpath:"C:/Libraries/libxml2-2.6.30.win32/lib/" libxml2.lib /libpath:"C:/Libraries/libxslt-1.1.26.win32/lib/" libxslt.lib /libpath:"C:/local/ismrmrd/ISMRMRD/lib/" ismrmrd.lib /libpath:"C:/Libraries/boost_1_55_0/lib32-msvc-12.0/" /DYNAMICBASE "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" "shell32.lib" "ole32.lib" "oleaut32.lib" "uuid.lib" "comdlg32.lib" "advapi32.lib"
    1. Use philips_to_ismrmrd.exe on another Windows 7 computer by gathering the following files into a single folder to copy to the other computer. Alternatively, use the philips_to_ismrmrd_exe tool designed for use on a Philips MRI Scanner console running Windows 7 (Philips MRI software release 5 or newer)
    C:\Libraries\philips_to_ismrmrd\philips_to_ismrmrd.exe
C:\Libraries\philips_to_ismrmrd\IsmrmrdPhilips.xsl
C:\local\HDF_Group\HDF5\1.8.15\bin\hdf5.dll
C:\Libraries\iconv-1.9.2.win32\bin\iconv.dll
C:\local\ismrmrd\ISMRMRD\lib\ismrmrd.dll
C:\Libraries\libxml2-2.6.30.win32\bin\libxml2.dll
C:\Libraries\libxslt-1.1.26.win32\bin\libxslt.dll
C:\local\ismrmrd\ISMRMRD\bin\mscvcp120.dll
C:\local\ismrmrd\ISMRMRD\bin\msvcr120.dll
C:\local\HDF_Group\HDF5\1.8.15\bin\szip.dll
C:\local\HDF_Group\HDF5\1.8.15\bin\zlib.dll
C:\Libraries\zlib-1.2.5\bin\zlib1.dll

Running the converter

Simple conversion:

philips_to_ismrmrd -f <PHILIPS FILE (without extenssion) > -x IsmrmrdPhilips.xsl -o philips.h5

Conversion with schema validation:

philips_to_ismrmrd -f <PHILIPS FILE (without extenssion) > -x IsmrmrdPhilips.xsl -s <PATH TO ISMRMRD SCHEMA> -o philips.h5