Scripts in CMTK, when referencing each other, are configured to use CMTK_INSTALL_DIR, which is /usr/local/.

At the same time, the tar archive has paths like this:

CMTK-3.2.0svn-Linux-x86_64/usr/local/bin/cmtk_functions.sh

We should do two things:

a) the archive should have paths like this:

CMTK-3.2.0svn-Linux-x86_64/bin/cmtk_functions.sh

such that we can untar directly into a convenient location.

b) within-CMTK references should be robust to installation under different roots. It is not clear to me right now how to best do that, though. Maybe we need to require users to set something like a "CMTKDIR" environment variable, like FSL does.

This should be fixed in CMTK 3.2.0.

CMTK_BINARY_DIR and CMTK_LIBRARY_DIR (if needed) can now be set before executing one of CMTK's scripts, and the script should use that to override whatever paths were defined during build time.

It's not automatic, but it should enable running CMTK from non-standard installation directories.