After some trials and errors and help from the MRtrix community, I managed to build MRtrix3 on Linux Fedora 24, so I thought I would share what worked for me.
So the first thing is that some the package names on Fedora are different from those given on the MRtrix Linux Installation page. Here are the packages that are needed for Fedora 24:
yum install git gcc-c++ python numpy eigen3-devel zlib-devel qt-devel mesa-libGL-devel
The second thing is that even though Qt’s moc (meta-object compiler) has been installed by the previous step, it is not on the path, so you need to set your PATH environment variable:
export PATH=/usr/lib64/qt4/bin:$PATH ./configure
The last thing is that using Qt4 didn’t work for me (see this post), so I had to install Qt5 and use that instead of Qt4:
yum install qt5-qtbase qt5-qtbase-devel qt5-qtsvg qt5-qtsvg-devel export PATH=/usr/lib64/qt5/bin:$PATH ./configure ./build
This did it for me.