For example, starting from a distribution with nothing already compiled:
make libmri.a 3dAutoTcorrelate
Virtually every program links to libmri.a, which is the library where all dataset, image processing, etc., utility functions written by us are stored.
Of course, you have to select a Makefile first. If you are on a system like mine, for example,
cp Makefile.macosx_10.5_Intel Makefile
and then edit Makefile to change the INSTALLDIR macro to some directory where you want binaries installed (only needed if you use 'make vastness' to compile and install).