In "Enhanced brain connectivity in long-term meditation practitioners", new MRI-based imaging techniques (diffusion tensor imaging) reveal large scale changes in structural connectivity throughout the brain, not just in specific locations.
Also stumbled across a study by Davidson, "Buddha's Brain: Neuroplasticity and Meditation" that describes some changes in the brain due to meditation. Davidson uses neutral language to describe shamatha meditation as FA or Focused Attention, and vipassana meditation as OM or Open Monitoring. Changes were measured with fMRI and EEG, and seem to relate to qualities of sustained attention (FA) as well as the ability of the brain to remain undisturbed by phenomena (OM). The latter reminds me of Pa Auk's instruction to create a mind inclined towards abandonment, a mind that can let go of its attachments.