Gadgetron / Discussion / General Discussion: Trying to convert .dat to hdf5 file

Matthew Robson - 2014-02-12

Hi guys,

I guess I am a bit rusty at all the stuff, but I am tenacious...

I am trying to build the tools that were posted on the Siemens IDEA forum for conversion of .dat (Siemens TWIX raw data files) into your HDF5 format.

So, from the siemens_mriclient directory I ran
cmake .
which completes.
And then I ran
Make

The make complains about missing a load of gadgetron....h files, which I have managed to hunt down and glue into this directory. But I can't manage to find the GadgetSocketSender.h anywhere (I have searched the whole Ubuntu install on y machine and it isn't anywhere to be seen).

I did an install of gadgetron (again) following the instructions in the wiki, but after wiping out the cache and cmaking again I get the same error.
What have I done wrong this time? I see there is a GadgetSocketSender file on sourceforge, but presumably I've mucked up and I don't feel confident to hack about.

I do seem to have some weird problem with java and matlab too, but I think these are unrelated, but thought I should flag it now just incase its relevant.

Thanks,

Matt

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- Michael Hansen - 2014-02-12
  
  Which package did you download from the idea board and what was the output of CMAKE?
  
  Sent from a mobile device - please excuse brevity and/or typos.
  
  On Feb 12, 2014, at 2:01 PM, "Matthew Robson" matt-oxford@users.sf.net wrote:
  
  Hi guys,
  
  I guess I am a bit rusty at all the stuff, but I am tenacious...
  
  I am trying to build the tools that were posted on the Siemens IDEA forum for conversion of .dat (Siemens TWIX raw data files) into your HDF5 format.
  
  So, from the siemens_mriclient directory I ran
  cmake .
  which completes.
  And then I ran
  Make
  
  The make complains about missing a load of gadgetron....h files, which I have managed to hunt down and glue into this directory. But I can't manage to find the GadgetSocketSender.h anywhere (I have searched the whole Ubuntu install on y machine and it isn't anywhere to be seen).
  
  I did an install of gadgetron (again) following the instructions in the wiki, but after wiping out the cache and cmaking again I get the same error.
  What have I done wrong this time? I see there is a GadgetSocketSender file on sourceforge, but presumably I've mucked up and I don't feel confident to hack about.
  
  I do seem to have some weird problem with java and matlab too, but I think these are unrelated, but thought I should flag it now just incase its relevant.
  
  Thanks,
  
  Matt
  
  Trying to convert .dat to hdf5 file
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  alternate
  
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  - Matthew Robson - 2014-02-13
    
    From IDEA
    
    GadgetronRelease_20120529
    
    I will remove it (and my magic glued files) and try again so you can share my cmake output.
    
    Matt
    
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    - Michael Hansen - 2014-02-13
      
      There is a package from Feb 2014, for use with the current release 2.5 of the Gadgetron. Use those.
      
      Sent from a mobile device - please excuse brevity and/or typos.
      
      On Feb 13, 2014, at 10:29 AM, "Matthew Robson" matt-oxford@users.sf.net wrote:
      
      From IDEA
      
      GadgetronRelease_20120529
      
      I will remove it (and my magic glued files) and try again so you can share my cmake output.
      
      Matt
      
      Trying to convert .dat to hdf5 file
      
      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
      
      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
      
      alternate
      
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    - Michael Hansen - 2014-02-13
      
      https://www.mr-idea.com/communities/idea/Lists/Customer/GadgetronArchive_20140211.zip
      
      If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Michael Hansen - 2014-02-12
  
  You should not need to "glue" anything in anywhere.
  
  Sent from a mobile device - please excuse brevity and/or typos.
  
  On Feb 12, 2014, at 2:01 PM, "Matthew Robson" matt-oxford@users.sf.net wrote:
  
  Hi guys,
  
  I guess I am a bit rusty at all the stuff, but I am tenacious...
  
  I am trying to build the tools that were posted on the Siemens IDEA forum for conversion of .dat (Siemens TWIX raw data files) into your HDF5 format.
  
  So, from the siemens_mriclient directory I ran
  cmake .
  which completes.
  And then I ran
  Make
  
  The make complains about missing a load of gadgetron....h files, which I have managed to hunt down and glue into this directory. But I can't manage to find the GadgetSocketSender.h anywhere (I have searched the whole Ubuntu install on y machine and it isn't anywhere to be seen).
  
  I did an install of gadgetron (again) following the instructions in the wiki, but after wiping out the cache and cmaking again I get the same error.
  What have I done wrong this time? I see there is a GadgetSocketSender file on sourceforge, but presumably I've mucked up and I don't feel confident to hack about.
  
  I do seem to have some weird problem with java and matlab too, but I think these are unrelated, but thought I should flag it now just incase its relevant.
  
  Thanks,
  
  Matt
  
  Trying to convert .dat to hdf5 file
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
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Matthew Robson - 2014-02-13

I will try the newer IDEA stuff. I was following the instructions in the manual when I got that file.

I am now following the wiki manual.

Last edit: Matthew Robson 2014-02-13

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- Michael Hansen - 2014-02-13
  
  Please use the latest archive from the idea board and the latest Gadgetron (2.5).
  
  Your versions don't match. The code you are using is 2 years old, that's like 85 in Gadgetron years;)
  
  I have deleted the older archives from the board to avoid confusion.
  
  Michael
  
  Sent from a mobile device - please excuse brevity and/or typos.
  
  On Feb 13, 2014, at 10:56 AM, "Matthew Robson" matt-oxford@users.sf.net wrote:
  
  Here you go. I have tried this again (without gluing files) and this time I didn't need to shuffle all those .h files around. But still the same socket error.
  
  I am new to the cmake command, previously I tried to cmake in the siemens_mriclient directory
  
  matt@matt-VirtualBox:~/GadgetronRelease_20120529/gt_siemens_apps$ mkdir build
  matt@matt-VirtualBox:~/GadgetronRelease_20120529/gt_siemens_apps$ cd build
  matt@matt-VirtualBox:~/GadgetronRelease_20120529/gt_siemens_apps/build$ cmake ../
  -- The C compiler identification is GNU
  -- The CXX compiler identification is GNU
  -- Check for working C compiler: /usr/bin/gcc
  -- Check for working C compiler: /usr/bin/gcc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Found Gadgetron: /usr/local/gadgetron
  CUDA_TOOLKIT_ROOT_DIR not found or specified
  -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
  -- Boost version: 1.46.1
  -- Found ACE library: /usr/lib/libACE.so
  -- Found ACE include: /usr/include
  -- Found HDF5: /usr/lib/libhdf5_cpp.so;/usr/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libm.so (Required is at least version "1.8")
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /home/matt/GadgetronRelease_20120529/gt_siemens_apps/build
  matt@matt-VirtualBox:~/GadgetronRelease_20120529/gt_siemens_apps/build$ cd ..
  matt@matt-VirtualBox:~/GadgetronRelease_20120529/gt_siemens_apps$ cd build
  matt@matt-VirtualBox:~/GadgetronRelease_20120529/gt_siemens_apps/build$ make
  Scanning dependencies of target siemens_mriclient
  [ 20%] Building CXX object siemens_mriclient/CMakeFiles/siemens_mriclient.dir/main.cpp.o
  /home/matt/GadgetronRelease_20120529/gt_siemens_apps/siemens_mriclient/main.cpp:13:87: fatal error: GadgetSocketSender.h: No such file or directory
  compilation terminated.
  make[2]: [siemens_mriclient/CMakeFiles/siemens_mriclient.dir/main.cpp.o] Error 1
  make[1]: [siemens_mriclient/CMakeFiles/siemens_mriclient.dir/all] Error 2
  make: *** [all] Error 2
  matt@matt-VirtualBox:~/GadgetronRelease_20120529/gt_siemens_apps/build$
  
  My installation followed this https://sourceforge.net/p/gadgetron/home/Linux%20Installation/
  I didn't install the MKL (as the text indicates it to be option)
  I did install the Armadillo (as the text suggests its compulsory), I hadn't done this previously.
  
  Then I moved onto the "Gadgetron Hello World" link. That works fine (although as I say viewing with matlab needs more work from me).
  
  Then I tried to read in some data of my own using the stuff from the IDEA site, and here we are....
  
  Trying to convert .dat to hdf5 file
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
  
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Matthew Robson - 2014-02-13

Right, 2014 version gets me a bit further.

matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps$ cd build
matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$ cmake ..
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found Gadgetron: /usr/local/gadgetron
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
-- Boost version: 1.46.1
-- Found the following Boost libraries:
-- thread
-- system
-- Found ACE library: /usr/lib/libACE.so
-- Found ACE include: /usr/include
-- Found HDF5: /usr/lib/libhdf5_cpp.so;/usr/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libm.so (Required is at least version "1.8")
-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so
-- Found LibXslt: /usr/lib/x86_64-linux-gnu/libxslt.so
-- Found Ismrmrd: /usr/local/ismrmrd/include
Use dynamic toolbox libray ...
-- Configuring done
-- Generating done
-- Build files have been written to: /home/matt/GadgetronArchive_20140211/gt_siemens_apps/build
matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$ make
Scanning dependencies of target tinyxml
[ 9%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxmlerror.cpp.o
[ 18%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxmlparser.cpp.o
[ 27%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxml.cpp.o
Linking CXX shared library libtinyxml.so
[ 27%] Built target tinyxml
Scanning dependencies of target siemens_mriclient
[ 36%] Building CXX object siemens_mriclient/CMakeFiles/siemens_mriclient.dir/main.cpp.o
/home/matt/GadgetronArchive_20140211/gt_siemens_apps/siemens_mriclient/main.cpp:24:29: fatal error: GadgetronCommon.h: No such file or directory
compilation terminated.
make[2]: *** [siemens_mriclient/CMakeFiles/siemens_mriclient.dir/main.cpp.o] Error 1
make[1]: *** [siemens_mriclient/CMakeFiles/siemens_mriclient.dir/all] Error 2
make: *** [all] Error 2
matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$

I resisted the urge to glue it from somewhere else!

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Michael Hansen - 2014-02-13
  
  What version of the Gadgetron code are you using?
  
  Sent from a mobile device - please excuse brevity and/or typos.
  
  On Feb 13, 2014, at 11:59 AM, "Matthew Robson" matt-oxford@users.sf.net wrote:
  
  Right, 2014 version gets me a bit further.
  
  matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps$ cd build
  matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$ cmake ..
  -- The C compiler identification is GNU
  -- The CXX compiler identification is GNU
  -- Check for working C compiler: /usr/bin/gcc
  -- Check for working C compiler: /usr/bin/gcc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Found Gadgetron: /usr/local/gadgetron
  CUDA_TOOLKIT_ROOT_DIR not found or specified
  -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
  -- Boost version: 1.46.1
  -- Found the following Boost libraries:
  -- thread
  -- system
  -- Found ACE library: /usr/lib/libACE.so
  -- Found ACE include: /usr/include
  -- Found HDF5: /usr/lib/libhdf5_cpp.so;/usr/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libm.so (Required is at least version "1.8")
  -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so
  -- Found LibXslt: /usr/lib/x86_64-linux-gnu/libxslt.so
  -- Found Ismrmrd: /usr/local/ismrmrd/include
  Use dynamic toolbox libray ...
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /home/matt/GadgetronArchive_20140211/gt_siemens_apps/build
  matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$ make
  Scanning dependencies of target tinyxml
  [ 9%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxmlerror.cpp.o
  [ 18%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxmlparser.cpp.o
  [ 27%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxml.cpp.o
  Linking CXX shared library libtinyxml.so
  [ 27%] Built target tinyxml
  Scanning dependencies of target siemens_mriclient
  [ 36%] Building CXX object siemens_mriclient/CMakeFiles/siemens_mriclient.dir/main.cpp.o
  /home/matt/GadgetronArchive_20140211/gt_siemens_apps/siemens_mriclient/main.cpp:24:29: fatal error: GadgetronCommon.h: No such file or directory
  compilation terminated.
  make[2]: [siemens_mriclient/CMakeFiles/siemens_mriclient.dir/main.cpp.o] Error 1
  make[1]: [siemens_mriclient/CMakeFiles/siemens_mriclient.dir/all] Error 2
  make: *** [all] Error 2
  matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$
  
  I resisted the urge to glue it from somewhere else!
  
  Trying to convert .dat to hdf5 file
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
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- Souheil Inati - 2014-02-13
  
  Do you GADGETRON_HOME defined?
  
  Souheil Inati, PhD
  Staff Scientist
  FMRI Facility
  NIMH/NIH/DHHS
  souheil.inati@nih.govsouheil.inati@nih.gov
  
  On Feb 13, 2014, at 11:59 AM, Matthew Robson matt-oxford@users.sf.netamp#109;amp#97;amp#116;amp#116;amp#45;amp#111;amp#120;amp#102;amp#111;amp#114;amp#100;amp#64;amp#117;amp#115;amp#101;amp#114;amp#115;amp#46;amp#115;amp#102;amp#46;amp#110;amp#101;amp#116; wrote:
  
  Right, 2014 version gets me a bit further.
  
  matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps$ cd build
  matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$ cmake ..
  -- The C compiler identification is GNU
  -- The CXX compiler identification is GNU
  -- Check for working C compiler: /usr/bin/gcc
  -- Check for working C compiler: /usr/bin/gcc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Found Gadgetron: /usr/local/gadgetron
  CUDA_TOOLKIT_ROOT_DIR not found or specified
  -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
  -- Boost version: 1.46.1
  -- Found the following Boost libraries:
  -- thread
  -- system
  -- Found ACE library: /usr/lib/libACE.so
  -- Found ACE include: /usr/include
  -- Found HDF5: /usr/lib/libhdf5_cpp.so;/usr/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libm.so (Required is at least version "1.8")
  -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so
  -- Found LibXslt: /usr/lib/x86_64-linux-gnu/libxslt.so
  -- Found Ismrmrd: /usr/local/ismrmrd/include
  Use dynamic toolbox libray ...
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /home/matt/GadgetronArchive_20140211/gt_siemens_apps/build
  matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$ make
  Scanning dependencies of target tinyxml
  [ 9%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxmlerror.cpp.o
  [ 18%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxmlparser.cpp.o
  [ 27%] Building CXX object dependencies/tinyxml/CMakeFiles/tinyxml.dir/tinyxml.cpp.o
  Linking CXX shared library libtinyxml.so
  [ 27%] Built target tinyxml
  Scanning dependencies of target siemens_mriclient
  [ 36%] Building CXX object siemens_mriclient/CMakeFiles/siemens_mriclient.dir/main.cpp.o
  /home/matt/GadgetronArchive_20140211/gt_siemens_apps/siemens_mriclient/main.cpp:24:29: fatal error: GadgetronCommon.h: No such file or directory
  compilation terminated.
  make[2]: [siemens_mriclient/CMakeFiles/siemens_mriclient.dir/main.cpp.o] Error 1
  make[1]: [siemens_mriclient/CMakeFiles/siemens_mriclient.dir/all] Error 2
  make: *** [all] Error 2
  matt@matt-VirtualBox:~/GadgetronArchive_20140211/gt_siemens_apps/build$
  
  I resisted the urge to glue it from somewhere else!
  
  Trying to convert .dat to hdf5 filehttps://sourceforge.net/p/gadgetron/discussion/general/thread/89746973/?limit=25#3123
  
  Sent from sourceforge.nethttp://sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
  
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  - Matthew Robson - 2014-02-13
    
    Sorry I didn't see this:
    
    If I type "env" then here is snippet.
    
    PATH=/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/matt/bin:/bin:/usr/local/gadgetron/bin:/usr/local/ismrmrd/bin:/usr/local/gadgetron/bin:/usr/local/ismrmrd/bin
    DESKTOP_SESSION=ubuntu-2d
    PWD=/home/matt/GadgetronArchive_20140211/gt_siemens_apps
    LANG=en_GB.UTF-8
    MANDATORY_PATH=/usr/share/gconf/ubuntu-2d.mandatory.path
    UBUNTU_MENUPROXY=libappmenu.so
    GDMSESSION=ubuntu-2d
    SHLVL=1
    HOME=/home/matt
    LANGUAGE=en_GB:en
    GNOME_DESKTOP_SESSION_ID=this-is-deprecated
    MATLAB_ROOT=/usr/local/matlabR2013b/bin
    ISMRMRD_HOME=/usr/local/ismrmrd
    LOGNAME=matt
    XDG_DATA_DIRS=/usr/share/ubuntu-2d:/usr/share/gnome:/usr/local/share/:/usr/share/
    DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-WdD1FeBwk9,guid=61b735edb72c965d296739380000000d
    LESSOPEN=| /usr/bin/lesspipe %s
    GADGETRON_HOME=/usr/local/gadgetron
    DISPLAY=:0
    XDG_CURRENT_DESKTOP=Unity
    LESSCLOSE=/usr/bin/lesspipe %s %s
    COLORTERM=gnome-terminal
    XAUTHORITY=/home/matt/.Xauthority
    _=/usr/bin/env
    OLDPWD=/home/matt/GadgetronArchive_20140211
    
    So that seems to be configured.
    
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- Michael Hansen - 2014-02-13
  
  GadgetronCommon.h should be in /usr/local/gadgetron/include, if you are using the latest version of the Gadgetron.
  
  Which version of the Gadgetron code are you building against?
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Matthew Robson - 2014-02-13

Not on mine.

The directory listing goes from Gadgettron.h straight to GadgetronConnector.h

Version wise. Yesterday I ran
git close git:://git.code.sf.net/p/gadgetron/gadgetron
and followed the instructions in the wiki manual from there.

I didn't manage to get matlab to play but it did make without it in the end.

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- Michael Hansen - 2014-02-13
  
  Hmmm....that is very strange. It should be installed from the "core" toolbox.
  
  Could you send me me the output of:
  
  cat $GADGETRON_SOURCE/toolboxes/core/CMakeLists.txt
  
  (replace GADGETRON_SOURCE with the location of your source). Mine looks like the dump below. As you can it, it should install that file in your include directory. I am a bit unsure about what version of the code you are using. When was the last time you did a "git pull origin" on the source to get the latest version from sourceforge?
  
  include_directories( ${Boost_INCLUDE_DIR} ) configure_file(core_defines.h.in ${CMAKE_CURRENT_SOURCE_DIR}/core_defines.h) install(FILES core_defines.h NDArray.h complext.h vector_td.h vector_td_operators.h vector_td_utilities.h vector_td_io.h real_utilities.h GadgetronCommon.h GadgetronException.h GadgetronTimer.h SerializableObject.h DESTINATION include) add_subdirectory(cpu) if (CUDA_FOUND) add_subdirectory(gpu) endif (CUDA_FOUND)
  
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Matthew Robson - 2014-02-13

When I tried the latest version of gadgetron (from the Download gadgetron_v2.5.0.tar.gz ) and extracted the files. The cmake wouldn't work because the cmakelist was preceded by the word gadgetron, so cmake couldn't find it (the README.txt file wasn't very helpful at that point). As I am a cmake virgin I tried plan-B which was the git thing. git is also a new thing on me. Lets hope the old phrase "you can't teach an old dog a new trick" doesn't hold up.

Matt

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- Michael Hansen - 2014-02-13
  
  What do you mean by "he cmakelist was preceded by the word gadgetron", totally confused here.
  
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- Michael Hansen - 2014-02-13
  
  Just replaced the tar file on the website to make sure, but the git archive should be working. Please check the CMakeLists file indicated above.
  
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Matthew Robson - 2014-02-13

No problem, this is a side point really, but was an explanation of why I was using the git approach to get at the files.

So. In ubuntu if I take the gadgetron_v2.5.0.ar.gz and right click, I can "Open with archive Manager". So if I do that and "Extract". then the directory listing looks like this:
matt@matt-VirtualBox:/media/windows-share/unpacked$ ls -l
total 27
drwxrwxrwx 1 root root 0 Jan 24 15:52 gadgetronapps
drwxrwxrwx 1 root root 4096 Jan 24 15:52 gadgetroncmake
-rwxrwxrwx 1 root root 7437 Feb 13 17:40 gadgetronCMakeLists.txt
drwxrwxrwx 1 root root 0 Jan 24 15:52 gadgetrondoc
drwxrwxrwx 1 root root 4096 Jan 24 15:52 gadgetrongadgets
-rwxrwxrwx 1 root root 173 Feb 13 17:40 gadgetron.gitignore
-rwxrwxrwx 1 root root 1752 Feb 13 17:40 gadgetronLICENSE
-rwxrwxrwx 1 root root 399 Feb 13 17:40 gadgetronREADME
drwxrwxrwx 1 root root 4096 Jan 24 15:52 gadgetrontest
drwxrwxrwx 1 root root 4096 Jan 24 15:52 gadgetrontoolboxes

typing "cmake . " fails

That is why I chose to follow the git instructions, which I thought had worked.

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Matthew Robson - 2014-02-13

Cool that change has fixed the cmakelist problem.
Now when I follow the steps above I get a more normal directory listing.

Should I make this "on top" of the previous version, or do I need to remove the previous version?

Matt

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Matthew Robson - 2014-02-13

Sorry, I am a bit crap at the terminology. I am sorry for that.

What I mean is.
Can I simply go through the
mkdir build
cd build
cmake ../
make
sudo make install

or do I have to do something first with the files that I put on here before?

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- Michael Hansen - 2014-02-13
  
  You should be able to just build on top, but to make sure you are starting from a clean slate, I could delete your old GADGETRON_SOURCE (wherever that is) folder. Then either unpack from the new tarball or use git to get the code and then:
  
  mkdir build
  cd build
  cmake ../
  make
  sudo make install
  
  Then check that your /usr/local/gadgetron/include folder has GadgetronCommon.h
  
  Then try to build the gt_siemens_apps again.
  
  We're getting closer, I think.
  
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  - Souheil Inati - 2014-02-13
    
    For what it's worth I always do a clean install and blow away /usr/local/gadgetron first.
    
    Sent with Good (www.good.com)
    
    -----Original Message-----
    From: Michael Hansen [hansenms@users.sf.nethansenms@users.sf.net]
    Sent: Thursday, February 13, 2014 01:15 PM Eastern Standard Time
    To: [gadgetron:discussion]
    Subject: [gadgetron:discussion] Re: Trying to convert .dat to hdf5 file
    
    You should be able to just build on top, but to make sure you are starting from a clean slate, I could delete your old GADGETRON_SOURCE (wherever that is) folder. Then either unpack from the new tarball or use git to get the code and then:
    
    mkdir build
    cd build
    cmake ../
    make
    sudo make install
    
    Then check that your /usr/local/gadgetron/include folder has GadgetronCommon.h
    
    Then try to build the gt_siemens_apps again.
    
    We're getting closer, I think.
    
    Trying to convert .dat to hdf5 filehttps://sourceforge.net/p/gadgetron/discussion/general/thread/89746973/?limit=25#80a9/b7ba
    
    Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
    
    To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
    
    alternate
    
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    - Michael Hansen - 2014-02-13
      
      I never do, but then again I'm a glutton for punishment;)
      
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Matthew Robson - 2014-02-13

You beauties.
GadgetronCommon.h in the correct place.
.dat converted to .hdf5

Thanks for your patience with me.

Matt

p.s. you might think its idiot proof, but you should never underestimate the creativity of idiots!

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Trying to convert .dat to hdf5 file

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Trying to convert .dat to hdf5 file

Do you GADGETRON_HOME defined?

Trying to convert .dat to hdf5 file

Medical Image Reconstruction Framework

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Trying to convert .dat to hdf5 file document.SUBSCRIPTION_OPTIONS = { "thing": "topic", "subscribed": false, "url": "subscribe", "icon": { "css": "fa fa-envelope-o" } };

Do you GADGETRON_HOME defined?

Trying to convert .dat to hdf5 file