/ge_to_ismrmrd

GE to ISMRMRD converter

Primary LanguageC++OtherNOASSERTION

Getting started with the Orchestra to ISMRMRD converter library

Orchestra conversion tools

To build and install the tools to convert GE raw files into ISMRMRD files:

  1. To use Orchestra's version 2 SDK to build ISMRMRD and GE-to-ISMRMRD, when trying to compile with the shipping configuration, an error message of:
   tlslayer.cc:(.text+0x1bed): undefined reference to `RAND_egd'

is generated on openSUSE 15.2. This happens because in current versions of OpenSSL, building the "Entropy Gathering Daemon" is disabled by default on openSUSE. However, since this function call is in a library shipping with Orchestra 2.0, then on openSUSE, OpenSSL must be built and installed into Orchestra's environment, with the appropriate option enabled.

To do this, first obtain the flags with which OpenSSL is built, by using the command:

   openssl version -f

On openSUSE 15.2, this output of this command is:

   compiler: gcc -fPIC -pthread -m64 -Wa,--noexecstack -Wall -O3 -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g -Wa,--noexecstack -fno-common -Wall -DOPENSSL_USE_NODELETE -DL_ENDIAN -DOPENSSL_PIC -DOPENSSL_CPUID_OBJ -DOPENSSL_IA32_SSE2 -DOPENSSL_BN_ASM_MONT -DOPENSSL_BN_ASM_MONT5 -DOPENSSL_BN_ASM_GF2m -DSHA1_ASM -DSHA256_ASM -DSHA512_ASM -DKECCAK1600_ASM -DRC4_ASM -DMD5_ASM -DVPAES_ASM -DGHASH_ASM -DECP_NISTZ256_ASM -DX25519_ASM -DPOLY1305_ASM -DNDEBUG -D_FORTIFY_SOURCE=2 -DTERMIO -DPURIFY -D_GNU_SOURCE -DOPENSSL_NO_BUF_FREELISTS

This command is then used to configure and build OpenSSL. First, obtain the last 1.0 version of OpenSSL (installed on GE's OS, and openSUSE 15.2), at this link.

Then configure OpenSSL to install into Orchestra's environment (with the "--prefix=$SDKTOP/3p" option), and with the "Entropy Gathering Daemon" option activated (with the "enable-egd" flag added), i.e.:

   ./config --prefix=$SDKTOP/3p enable-egd -fPIC -pthread -m64 -Wa,--noexecstack -Wall -O3 -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g -Wa,--noexecstack -fno-common -Wall -DOPENSSL_USE_NODELETE -DL_ENDIAN -DOPENSSL_PIC -DOPENSSL_CPUID_OBJ -DOPENSSL_IA32_SSE2 -DOPENSSL_BN_ASM_MONT -DOPENSSL_BN_ASM_MONT5 -DOPENSSL_BN_ASM_GF2m -DSHA1_ASM -DSHA256_ASM -DSHA512_ASM -DKECCAK1600_ASM -DRC4_ASM -DMD5_ASM -DVPAES_ASM -DGHASH_ASM -DECP_NISTZ256_ASM -DX25519_ASM -DPOLY1305_ASM -DNDEBUG -D_FORTIFY_SOURCE=2 -DTERMIO -DPURIFY -D_GNU_SOURCE -DOPENSSL_NO_BUF_FREELISTS

After the OpenSSL build configuration is complete, then running:

   make
   make install

(from an environment with the appropriate system permissions) will build and install OpenSSL into Orchestra, so that ISMRMRD, and GE-to-ISMRMRD finds all required components, and successfully builds. Continue with the steps previously outlined below, to build and install ISMRMRD, and GE-to-ISMRMRD.

  1. Define the SDKTOP environment variable:

    export SDKTOP=/fmrif/projects/ESE/Orchestra

  2. Define the ISMRMRD_HOME AND GE_TOOLS_HOME variables. These specify installation location(s), e.g.

    export ISMRMRD_HOME=<prefix>/ismrmrd
export GE_TOOLS_HOME=<prefix>/ge-tools

  3. Obtain the ISMRMRD source code:

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

  4. Pre-define the location of HDF5 in order to use Orchestra's static HDF5 library:

    export HDF5_ROOT=$SDKTOP/3p

    Any other version of HDF5 on the system can cause conflicts as cmake will find all versions, and will cause issues or conflicts with the build process. For these instructions to work, only the HDF5 supplied with Orchestra should be on the system.

  5. Configure, compile, and install ISMRMRD:

    cd ismrmrd/
mkdir build
cd build/
cmake -D build4GE=ON -D CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME ..
make install
cd ../

    If the situation is encountered where the system compilers and Boost version are "too far ahead" of how Orchestra's support libraries (which include Boost) were compiled, then it may be necessary to have the ISMRMRD build explicitly refer to Orchestra's Boost libraries, with a command like:

    cmake -D CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME -D build4GE=TRUE -D Boost_NO_BOOST_CMAKE=TRUE -D Boost_NO_SYSTEM_PATHS=TRUE ..

    A good discussion of pointing cmake to alternate Boost installations can be found at this link.

    It may also be necessary to force the usage of older ABIs standards for C++. To accomplish this, a switch along the lines of:

    -D_GLIBCXX_USE_CXX11_ABI=0

    will have to be added to the "CMAKE_CXX_FLAGS" option in the project's CMakeLists.txt file.

  6. If using the Gadgetron for reconstruction, please use a standard Gadgetron installation or Docker container. The Gadgetron now requires Boost version 1.65 or newer, which is newer than that supplied with GE's latest Orchestra Linux SDK. Therefore, Gadgetron currently cannot be built using components from GE's Orchestra Linux SDK, as was previously possible.

  7. Obtain the GE converter source code:

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

  8. Configure, compile and install the converter:

    cd ge_to_ismrmrd/
mkdir build
cd build/
cmake -D CMAKE_INSTALL_PREFIX=$GE_TOOLS_HOME ..
make install
cd ../

  9. Make sure $ISMRMRD_HOME/bin and $GE_TOOLS_HOME/bin are added to your environment's PATH variable, and that $ISMRMRD_HOME/lib and $GE_TOOLS_HOME/lib are added to your environment's LD_LIBRARY_PATH variable, to be able to use the libraries and binaries supplied with these tools.

  10. A typical command line to convert the supplied P-file using this library is:

    ge2ismrmrd -v P21504_FSE.7

  11. If customized conversion libraries and/or stylesheets are desired, the corresponding command will be:

    ge2ismrmrd -v -p NIH2dfastConverter -x $GE_TOOLS_HOME/share/ge-tools/config/default.xsl P21504_FSE.7

    The source code that enables this example is included with these tools. This example is a straightforward copy of the GenericConverter, but it shows how these classes can be inherited from and implemented.

  12. Similarly, a typical command line to convert an example ScanArchive file using this library is:

    ge2ismrmrd -v -p GenericConverter -x $GE_TOOLS_HOME/share/ge-tools/config/default.xsl ScanArchive_FSE.h5

    Sample raw data files are now in the 'sampleData' directory.