Just a quick follow up on my last post.
In my previous post, qmake was not found, because is was linked to /usr/bin/qmake-4.8.
I fixed that, and redid the build. It got much farther, and I had my hopes.
However, it finished with:

Find file [bin/plugins/data_IO/load_image_using_Bioformats/loci_tools.jar]
The application cannot be opened because its executable is missing.

The last line happens because it tries to launch vaa3d, and this was not built.

Here are other errors I found in the output of build

make: *** [clean] Error 1

make: *** [v3d_plugin_loader.o] Error 1
make: *** Waiting for unfinished jobs....

make: *** No rule to make target `../../../../brainaligner/jba/c++/jba_mainfunc.cpp', needed by `jba_mainfunc.o'.  Stop.
make: *** Waiting for unfinished jobs...

make: *** [moc_mapviewer.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [mapviewer.o] Error 1

make: *** [regiongrow.o] Error 1
make: *** Waiting for unfinished jobs....

That is all I found.

--aryeh