Stefan Röttger

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Working with PVM and DICOM

Exercise (1a)

• We assume that you are familiar with Linux and the Unix shell.
• First, we learn how to compile Open-source software packages.
• Then, we install the following dependencies: g++ cmake freeglut3-dev libqt4-dev
  • Also see the hints for Linux and MacOS X at the bottom of this page.
• And finally, we checkout the VVV software via svn and build the package:
  • svn co http://svn.code.sf.net/p/volren/code/viewer vvv
    • We use CMake style: cmake . && make

Exercise (1b)

• Try the “pvmplay” tool as part of the VVV package with the following CT and MRI datasets from the Volume Library:
  • http://schorsch.efi.fh-nuernberg.de/data/volume/CT-Head.pvm
  • http://schorsch.efi.fh-nuernberg.de/data/volume/MRI-Head.pvm
• You will find the tool in the “tools” directory.
• Run the tool from the command line with the above data sets as additional command line argument.
  • After loading the above volume data, scroll through the displayed slices by hitting space - or +.
  • Where can we see the skull in the images?
• Extract slice number 10 of the CT data set with the command line tool “pvmplay” (run it without arguments to see its usage and command line options).
  • Open the slice with Imagemagick and convert to PNG (using the “display” or “convert” tool of ImageMagick).
• Now we would like to visualize the bone structure by painting those structures red:
  • Convert the greyscale image to RGB and replace gray values above 200 ($\approx 80%$) with red (use an image manipulation application of your choice).
  • Can we find a threshold value, which masks the bone better?
• Print out the colored slice and submit it.

Home work (1c)

• Download DCMTK and install the package
  • Either use the DCMTK 3.6.0 release (Ubuntu 14.04)
    • http://dicom.offis.de/download/dcmtk/dcmtk360/dcmtk-3.6.0.tar.gz
  • Or one of the latest release snapshots (Ubuntu 16.04 LTS, MacOS X):
    • http://dicom.offis.de/download/dcmtk/snapshot
  • To build use CMake style:
    • cmake -DDCMTK_WITH_ICU=OFF . && make && sudo make install
• Try the “dcmdump” tool from the bin directory with the following DICOM images:
  • DicomImage1.dcm DicomImage2.dcm
  • How many pixels with how many bytes does it contain?
  • Google for a program, which can be used to display DICOM images.
  • Open the images, and determine what the images show!
• Print the output of dcmdump and submit it to your advisor.

Notes for Ubuntu users:

• You need to install the following packages: g++ cmake cmake-curses-gui freeglut3-dev mesa-utils libqt4-dev libz-dev
• Hint for Ubuntu 14.04 LTS: Due to a linker bug, the dynamic linker will crash on any OpenGL program (like pvmplay), if you have the NVIDIA graphics drivers installed. Ubuntu 15.04 and 16.04 LTS is not affected. For 14.04 LTS use one of the following workarounds:
  • Remove the NVIDIA drivers: sudo apt-get remove nvidia-331
  • Preload the Mesa drivers: export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1
  • Use Ubuntu 16.04 LTS

Notes for OpenSuse users:

• Required dependencies: g++ cmake freeglut-devel libqt4-devel libz-devel

Notes for MacOS X users:

• It is recommended to install cmake and libz from source!
• Or use brew to install any missing dependencies!

Notes for VirtualBox users:

• If you are using VirtualBox or experience problems with your graphics hardware, you need to activate the OpenGL software rasterizer:

export LIBGL_ALWAYS_SOFTWARE=1

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