OK, good to hear. For reference, you can copy-paste the following into a terminal, having changed into the MRtrix3 folder - it should just work as-is…
wget http://bitbucket.org/eigen/eigen/get/3.2.8.tar.gz
tar xvfz 3.2.8.tar.gz
rm -f 3.2.8.tar.gz
mv eigen-eigen-* eigen
EIGEN_CFLAGS="-isystem $(pwd)/eigen" ./configure
./build