Visualization tools

Currently GAMOS does not include any utility to visualize the reconstructed images (or projection data), instead of it, we recommend the installation of one of the following free programs to visualize or analyze images: AMIDE and ImageJ.

AMIDE 25 is a free tool for viewing, analyzing, and registering volumetric medical imaging data sets. It has been written on top of GTK+, and runs on any system that supports this toolkit, including Linux. Both *.hv and *.hdr image header files can be opened by AMIDE, using the option: File -> Import File (guess). AMIDE also is also recommended to visualize STIR images.

ImageJ 26 is an image processing tool written in Java, which allows it to run on Linux, Mac OS X and Windows. ImageJ and its Java source code are freely available and in the public domain. To open *.hv images the program needs a plug-in to read Interfile formats; next it is described how to install its version 1.44 (bundled with 32-bit Java), with the Interfile decoder plug-in, in Linux:


      # Installing ImageJ
      cd ${HOME}
      wget http://rsb.info.nih.gov/ij/download/linux/ij144-x86.tar.gz
      gunzip ij144-x86.tar.gz
      tar xvf ij144-x86.tar
      # Installing plug-in (.jar file) to read Interfile images
      cd ImageJ/plugins
      wget http://www.med.harvard.edu/JPNM/ij/plugins/download/Interfile_TP.jar
      cd ..
    

To run ImageJ execute the './run' script. Images with extension .hv can be opened by the "NucMed Open" command (in menu Plugins->NucMed), alternatively the user can open it ("MY_IMAGE.hv") from the command line using the following expression:


      ${HOME}/ImageJ/jre/bin/java -Xmx512m -jar ${HOME}/ImageJ/ij.jar 
      -ijpath ${HOME}/ImageJ -eval "run('NucMed Open', 'open=MY_IMAGE.hv');