How different meditation techniques affect the brain
Three major types of practices have been classified according to EEG pattern and the type of cognitive processing (or mental activity) involved: 1) controlled focus (concentration), 2) open monitoring (mindfulness type practices), and 3) automatic self-transcending (such as Transcendental Meditation). Each type of meditation engages the mind in a very different way and has a specific EEG pattern.
Neuroscience have discovered that concentration techniques, such as many Zen practices that involve controlled focus, typically show strong gamma waves (Lutz A, et al, 2004).
Mindfulness meditation (or open monitoring) typically produces frontal theta, an EEG pattern associated with memory tasks and internal focus (Cahn, Delorme, & Polich, 2010).
The Transcendental Meditation technique has been shown (in both new long-term meditators) to consistently produce high alpha coherence in the prefrontal cortex and throughout the rest of the brain (Travis et al, "Cognitive Processing," 11, 1, 2010.). Alpha waves are associated with a relaxed yet alert state of mind, and heightened coherence indicates increased efficiency of brain functioning.
Also, the scientific literature shows that different practices consistently produce measurably different results regarding levels of rest, reduction of anxiety and depression, and effects on health and self-actualization. Often research on one meditation technique is wrongly attributed to another. When choosing a meditation technique, it is advised to look into the scientific research, if any, done on that specific technique. Pubmed.org is a good source in general and doctorsontm.org presents research on the TM technique.