MITK works normally again after removing the .local/share/data/DKFZ/ folder.
Obiviously some settings were defective.

Console output

This might be of further interest:
AD\intemann@e010pc35:/opt/MITK-Diffusion-2012.09/bin$ ldd mitkDiffusion
linux-vdso.so.1 => (0x00007fff041d1000)
liborg_blueberry_osgi.so => /opt/MITK-Diffusion-2012.09/bin/plugins/liborg_blueberry_osgi.so (0x00007f1c6337f000)
libQtNetwork.so.4 => /usr/lib/x86_64-linux-gnu/libQtNetwork.so.4 (0x00007f1c6300b000)
libPocoUtil.so.1.3.5 => /opt/MITK-Diffusion-2012.09/bin/libPocoUtil.so.1.3.5 (0x00007f1c62db9000)
libPocoFoundation.so.1.3.5 => /opt/MITK-Diffusion-2012.09/bin/libPocoFoundation.so.1.3.5 (0x00007f1c62a24000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f1c62806000)
libQtGui.so.4 => /usr/lib/x86_64-linux-gnu/libQtGui.so.4 (0x00007f1c61b38000)
libQtCore.so.4 => /usr/lib/x86_64-linux-gnu/libQtCore.so.4 (0x00007f1c61666000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f1c61365000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f1c6114f000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1c60d90000)
libCTKPluginFramework.so.0.1 => /opt/MITK-Diffusion-2012.09/bin/libCTKPluginFramework.so.0.1 (0x00007f1c60af9000)
libmbilog.so => /opt/MITK-Diffusion-2012.09/bin/libmbilog.so (0x00007f1c608f4000)
libPocoXML.so.1.3.5 => /opt/MITK-Diffusion-2012.09/bin/libPocoXML.so.1.3.5 (0x00007f1c6065f000)
libCTKCore.so.0.1 => /opt/MITK-Diffusion-2012.09/bin/libCTKCore.so.0.1 (0x00007f1c603eb000)
libQtOpenGL.so.4 => /usr/lib/x86_64-linux-gnu/libQtOpenGL.so.4 (0x00007f1c600ed000)
libQtXml.so.4 => /usr/lib/x86_64-linux-gnu/libQtXml.so.4 (0x00007f1c5feaa000)
libQtSql.so.4 => /usr/lib/x86_64-linux-gnu/libQtSql.so.4 (0x00007f1c5fc6a000)
libQtXmlPatterns.so.4 => /usr/lib/x86_64-linux-gnu/libQtXmlPatterns.so.4 (0x00007f1c5f620000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f1c5f41c000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f1c5f213000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f1c5ef17000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f1c5ed00000)
/lib64/ld-linux-x86-64.so.2 (0x00007f1c6361f000)
libfontconfig.so.1 => /usr/lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007f1c5eac9000)
libaudio.so.2 => /usr/lib/x86_64-linux-gnu/libaudio.so.2 (0x00007f1c5e8b1000)
libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f1c5e5bb000)
libpng12.so.0 => /lib/x86_64-linux-gnu/libpng12.so.0 (0x00007f1c5e393000)
libfreetype.so.6 => /usr/lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f1c5e0f7000)
libgobject-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0 (0x00007f1c5dea7000)
libSM.so.6 => /usr/lib/x86_64-linux-gnu/libSM.so.6 (0x00007f1c5dc9f000)
libICE.so.6 => /usr/lib/x86_64-linux-gnu/libICE.so.6 (0x00007f1c5da85000)
libXi.so.6 => /usr/lib/x86_64-linux-gnu/libXi.so.6 (0x00007f1c5d875000)
libXrender.so.1 => /usr/lib/x86_64-linux-gnu/libXrender.so.1 (0x00007f1c5d66b000)
libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f1c5d45a000)
libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f1c5d125000)
libGL.so.1 => /usr/lib/nvidia-experimental-310/libGL.so.1 (0x00007f1c5ce03000)
libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f1c5cbd8000)
libXt.so.6 => /usr/lib/x86_64-linux-gnu/libXt.so.6 (0x00007f1c5c972000)
libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f1c5c76e000)
libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f1c5c531000)
libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 (0x00007f1c5c329000)
libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007f1c5c123000)
libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f1c5bf05000)
libnvidia-tls.so.310.14 => /usr/lib/nvidia-experimental-310/tls/libnvidia-tls.so.310.14 (0x00007f1c5bd01000)
libnvidia-glcore.so.310.14 => /usr/lib/nvidia-experimental-310/libnvidia-glcore.so.310.14 (0x00007f1c5980d000)
libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f1c59606000)

screenshot

Using Ubuntu 12.04 LTS.

Screenshot

I put some sample data into
smb://dkfzfsg/e011-projekte/Patientenstudien/Diffusion-Prostata