Quantitative Magnetization Transfer (qMT) Imaging allows quantification of parameters describing the macromolecular component of tissues, potentially specific for myelin in the central nervous system. To date, applications of qMT in small structures (e.g. the spinal cord) have been hampered by prohibitively long acquisition. We present a framework for robust qMT examinations in small structures. It consists of: a dedicated MT-weighted sequence for reduced field-of-view imaging, explicit modelling of the non-steady state signal, and optimal definition of the sampling scheme. Superiority of the framework compared to a conventional qMT protocol is demonstrated in the healthy spinal cord and in the brainstem.