Yoga is a system of physical of psychospiritual practices in vogue in South Asian sub-continent for more than three thousand years. Major advances in in vivo brain imaging, made possible by technological advances in functional MRI (fMRI) and PET scanning, have considerably advanced the scope for in-depth scientific studies on yoga. The most significant advancement in the study of the functioning of the human brain has been the development of the concept of “Blood Oxygenation Level Dependent” (BOLD) and its successful exploitation to image functionally activated brain regions through MRI. Ongoing developments in the techno-science of fMRI seems to open up hitherto unimagined prospects to study human brain in situ to understand the neurobiologic correlates of purely subjective experiences such as sense-perception, cognitive and affective behavioral states, as well as differing states of consciousness including sleep. An effective approach to achieve objectivisation of the predominantly subjective experience along the path of progress in yoga is by nudging neurobiologists to adopt clearly definable systems of yoga practice and to try and understand their neurobiological correlates (basic). Those who go through yogic progression with neurobiological insights can discern that psycho-physical practices like pranayama and dhyana are both energizing and transforming in a psycho-somatic sense—and that the major anatomical substrate for such transformation is brain stem. Functionally and anatomically definable subcortical systems involved in these yogic phenomena can be studied appropriately if technical requirements of the type referred to above are achievable to facilitate mini or micro-functional imaging of brainstem of evolving yogis.