Gadgetron  (Homebrew  +  Clang) Monday,  9  March  2015

12:02  PM

This is the Homebrew version of the installation: • • • • •

/usr/local is owned by the main user root (and sudo) are not used

Homebrew's python 2.7 is installed Using Matlab R2013b and Java 7 from Oracle GPU features are NOT supported

Prerequisites

1. Install Xcode 2. Install OS X Command Line Tools on the terminal: xcode-­‐select  -­‐-­‐install

3. Install Homebrew and check that it's working 4. Set environment variables in ~/.bash_profile or its equivalent #  Put  homebrew  paths  first export  PATH=/usr/local/bin:/usr/local/sbin:$PATH

#  Python export  PYTHONHOME=/usr/local/Frameworks/Python.framework/Versions/2. export  PYTHONPATH=$PYTHONHOME/lib/python2.7/site-­‐packages export  PYTHONPATH=/usr/local/opt/libxml2/lib/python2.7/site-­‐packages: #  MATLAB,  ISMRMRD,  GADGETRON export  MATLAB_HOME=/Applications/MATLAB_R2013b.app export  ISMRMRD_HOME=/usr/local export  GADGETRON_HOME=/usr/local/gadgetron export  PATH=$MATLAB_HOME/bin:$PATH export  PATH=$ISMRMRD_HOME/bin:$PATH export  PATH=$GADGETRON_HOME/bin:$PATH

export  DYLD_FALLBACK_LIBRARY_PATH=$ISMRMRD_HOME/lib export  DYLD_FALLBACK_LIBRARY_PATH=$GADGETRON_HOME/lib:$DYLD_FALLBACK export  DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH:$MATLA

5. Add the brew science formulae and the python formulae brew  tap  homebrew/science brew  tap  Homebrew/python

.7

s:$PYTHONPATH

K_LIBRARY_PATH AB_HOME/bin/maci64

export  DYLD_FALLBACK_LIBRARY_PATH=$GADGETRON_HOME/lib:$DYLD_FALLBACK export  DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH:$MATLA

5. Add the brew science formulae and the python formulae brew  tap  homebrew/science brew  tap  Homebrew/python

6. Install ISMRMRD and Gadgetron dependencies (build dcmtk from src)

brew  install  wget  cmake  boost  qt  fftw  swig  glew  ace  armadillo  dcmtk d xsl  fop brew  install  hdf5  -­‐-­‐enable-­‐cxx brew  install  python  boost-­‐python  numpy  scipy brew  install  matplotlib  -­‐-­‐with-­‐pygtk  -­‐-­‐with-­‐pyqt brew  install  wxpython  (SAH  Added  for  libxml2) brew  install  libxml2  -­‐-­‐with-­‐python pip  install  h5py  pyxb  Cython

7. pip  install  ismrmrd 8. Install GTest

wget  https://googletest.googlecode.com/files/gtest-­‐1.7.0.zip unzip  gtest-­‐1.7.0.zip cp  -­‐r  gtest-­‐1.7.0/include/gtest  /usr/local/include/. cd  gtest-­‐1.7.0 mkdir  build cd  build cmake  .. make cp  libgtest*  /usr/local/lib/.

9. Future Step: Install CUDA and CULA

10. Make sure you are using the same JDK as the Matlab Java version. In th determine your version like so: ○ javac  -­‐version on the command line ○ version  -­‐java in Matlab

For Matlab R2013b I used http://download.oracle.com/otn-pub/java b13/jdk-7u51-macosx-x64.dmg

Installation  from  Sources DCMTK brew install libiconv brew link libiconv (will fail) sudo brew link libiconv --force (will refuse, but allow sudo on next cmd) brew link libiconv --force (will work) ln -s /usr/local/lib/libiconv.2.dylib /usr/local/lib/liblibiconv.2.dylib ln -s /usr/local/lib/libiconv.dylib /usr/local/lib/liblibiconv.dylib git clone git://git.dcmtk.org/dcmtk.git cd dcmtk

K_LIBRARY_PATH AB_HOME/bin/maci64

doxygen  docbook-­‐

heory you can

a/jdk/7u51-

brew link libiconv (will fail) sudo brew link libiconv --force (will refuse, but allow sudo on next cmd) brew link libiconv --force (will work) ln -s /usr/local/lib/libiconv.2.dylib /usr/local/lib/liblibiconv.2.dylib ln -s /usr/local/lib/libiconv.dylib /usr/local/lib/liblibiconv.dylib git clone git://git.dcmtk.org/dcmtk.git cd dcmtk mkdir build cd build cmake make install

ISMRMRD

git  clone  https://github.com/ismrmrd/ismrmrd cd  ismrmrd git  checkout  development mkdir  build cd  build/ cmake  -­‐D  CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME  ../ make make  install Gadgetron

git  clone  https://github.com/gadgetron/gadgetron cd  gadgetron git  checkout  development mkdir  build cd  build/ cmake  -­‐DCMAKE_INSTALL_PREFIX=/usr/local  -­‐DPYTHON_LIBRARY=`python-­‐config  -­‐-­‐ DPYTHON_INCLUDE_DIR=`python-­‐config  -­‐-­‐prefix`/Headers  ../ make make  install Siemens converter (needed for Gadgetron integration tests)

git  clone  https://github.com/nih-­‐fmrif/siemens_to_ismrmrd cd  siemens_to_ismrmrd mkdir  build cd  build/ cmake  -­‐D  CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME  ../ make make  install GE tools (optional)

git  clone  https://github.com/nih-­‐fmrif/ge-­‐tools    (NOT  FOUND) cd  ge-­‐tools mkdir  build cd  build/ cmake  -­‐D  CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME  ../ make make  install

-­‐prefix`/Python  -­‐

git  clone  https://github.com/nih-­‐fmrif/ge-­‐tools    (NOT  FOUND) cd  ge-­‐tools mkdir  build cd  build/ cmake  -­‐D  CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME  ../ make make  install Post-install Config and Testing

1. Copy $GADGETRON_HOME/config/gadgetron.xml.example to$GADGETRON_HOME/co 2. Fetch  Gadgetron  test  data:  run python  get_data.py in test/integration in  the  Ga 3. Run  integration  tests:  run python  run_all_tests.py  $ISMRMRD_HOME  $GADGETRON test_cases.txt in test/integration in  the  Gadgetron  source  tree. Everything  works

onfig/gadgetron.xml

adgetron  source  tree.

N_HOME