If installing from sources, the configure script won't look for dependencies using the same database 'apt-get' is using.
Perhaps you already have the required dependencies, (since you installed all the deb files above) but can't be found by 'wajig' or 'apt-get'.
You could give it a try and see if it's working. There won't be any changes to your system until you run 'make install' anyway.
I downloaded the source and there is no configure file (I used 'find | grep configure' command). There is python program and as suggested by install.txt I copied 'invesalius' folder to /usr/lib/python2.7/site-packages (2.5 suggested in install.txt, while I have 2.7 and 3.2 versions). On running 'python invesalius.py' there were errors: first wxversion- which I installed, but then it asked for wx and others. I give up.
I am surprised that windows exe file installs in not only almost all versions of windows, but also in almost all distros of linux (with wine installed). While linux version does not even install on a very similar distribution for which it was released! I think this needs attention of the bigwigs of linux if they want linux to be for the users rather than for computer geeks only. One cannot expect authors of applications to release versions not only for each linux distro but for each of the distro's version (IMHO). Though most of the routinely required software like office applications works well on all distros, but it may take some time for specialized applications to be working everywhere on linux.
Do I have a better chance of this application working on Debian-stable (I am currently using Debian-testing)? What are the chances that problems will be less on an RPM based distribution like scientific linux ?
Is there any chance that auto-apt or autodeb may work here? It seems to be a python package. Auto-apt is there in debian-testing repository available for installation (about 50 mb package).
I see that developers are already trying to get invesalius to work well under Debian. (I cannot put URLs here at present but links are easily available on google).