An expert system is included in a downhole processor designed to acquire and process NMR data downhole in real time. The downhole processor controls the acquisition of the NMR data based at least in part on instructions transmitted downhole from a surface location and at least in part on evaluation of downhole conditions by the expert system. The downhole conditions include drilling operation conditions (including motion sensors) as well as lithology and fluid content of the formation obtained from other MWD data. The wait time, number of echos, number of repetitions of an echo sequence, interecho time, bandwidth and shape of the tipping and refocusing pulses may be dynamically changed. Data processing is a combination of standard evaluation techniques. Selected data and diagnostics are transmitted uphole. The expert system may be implemented as a two stage neural net. The first stage does the formation evaluation and the second stage controls the NMR pulse sequence.