> So if I do choose to download my own version of VTK 5.6.1, ITK 3.20 and GDCM
> 2.0.18 and build it myself I am wondering the steps needed to make it work.

>From GDCM 2.0.14 is used currently. You can check the versions in the
CMakeExternals directory.

You do not need to turn off the superbuild. There is a check in the
CMake files if the ITK_DIR, VTK_DIR etc. variables are set, and if
yes, that version will be used. It is useful if you want to use your
own build from ITK or VTK but you do not want to take care about the
others.

If you want a custom version from these projects, you have to build
these in advance, and the variables have to point to their binary
directory.

I found this page useful:
http://docs.mitk.org/nightly-qt4/BuildInstructionsPage.html

Best regards,
Miklos

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