Ok, so
"cmake ../cmtk-core"
worked I think, and then
"make"
worked for a bit until I got:

[ 38%] Building CXX object libs/System/CMakeFiles/cmtkSystem.dir/cmtkMemory.cxx.o
[ 38%] Building CXX object libs/System/CMakeFiles/cmtkSystem.dir/cmtkMountPoints.cxx.o
[ 38%] Building CXX object libs/System/CMakeFiles/cmtkSystem.dir/cmtkProgress.cxx.o
[ 38%] Building CXX object libs/System/CMakeFiles/cmtkSystem.dir/cmtkProgressConsole.cxx.o
[ 39%] Building CXX object libs/System/CMakeFiles/cmtkSystem.dir/cmtkRegressionTracker.cxx.o
[ 39%] Building CXX object libs/System/CMakeFiles/cmtkSystem.dir/cmtkStackBacktrace.cxx.o
[ 39%] Building CXX object libs/System/CMakeFiles/cmtkSystem.dir/cmtkStrUtility.cxx.o
[ 39%] Building CXX object libs/System/CMakeFiles/cmtkSystem.dir/cmtkThreads.cxx.o
In file included from /home/rportugues/cmtk/core/libs/System/cmtkThreads.cxx:75:0:
/home/rportugues/cmtk/core/libs/System/cmtkFFTW.h:36:19: fatal error: fftw3.h: No such file or directory
compilation terminated.
libs/System/CMakeFiles/cmtkSystem.dir/build.make:655: recipe for target 'libs/System/CMakeFiles/cmtkSystem.dir/cmtkThreads.cxx.o' failed
make[2]: *** [libs/System/CMakeFiles/cmtkSystem.dir/cmtkThreads.cxx.o] Error 1
CMakeFiles/Makefile2:4714: recipe for target 'libs/System/CMakeFiles/cmtkSystem.dir/all' failed
make[1]: *** [libs/System/CMakeFiles/cmtkSystem.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2
 
Does this mean anything to you?