About the Author: Fred Travis, Ph.D. is the Director of the Center for Brain, Consciousness, and Cognition, and an Associate Professor of Maharishi Vedic Science at Maharishi University of Management.
There are many systems of meditation that widely differ from one another in their procedures, contents, objects, beliefs, and goals. Given these differences, it is not surprising that research has shown they have different subjective and objective effects. Scientific research on one type of meditation cannot be generalized to effects from any type of meditation.
Let us compare three forms of meditation. Scientific research on the functioning of the brains of practitioners of these techniques have been published in peer-reviewed journals. The three forms in this document are: Mindfulness Meditation (also called Insight Meditation or Vipassana), Tibetan Buddhist Tsonghakapa, and the Transcendental Meditation® technique from the ancient Vedic tradition of India. These three methods have different procedures, different neural images (pictures of the brain or brain functioning), and different EEG patterns (electrical activity of the brain).
|Type of Meditation
|Insight, Vipassana, Mindfulness
||Observation [Reference 1]
|Transcendental Meditation Technique
||Effortless Transcending 
Different Neural Images
The neural images of different types of meditation are distinctly different. Brain blood flow and brain metabolic rate can be imaged with modern neural imaging techniques using MRI (Magnetic Resonance Imaging) or PET (Positron Emission Tomography). These data are from independent labs reports and published research.
Type of Meditation: Mindfulness
Neural Images: Thicker right insula, thicker right frontal, thicker sensory 
Explanation: Higher gray matter volume—more connections—are reported in areas used in focusing of attention (right frontal areas) and brain areas involved with sensory perception: the right insula (taste and emotionally relevant context), right parietal (touch) and right temporal (hearing). Thicker cortex suggests these local areas are used during Mindfulness.
Type of Meditation: Tibetan Buddhism
Neural Images: Activity in the frontal (left) increases; activity in the thalamus increases; activity in the parietal lobe decreases. 
Explanation: In Tibetan Buddhist Tsonghakapa meditation, activity in the frontal lobe increases—this is what happens when focusing. Activity increases in the thalamus, the gateway of activation to the brain. Activity decreases in the parietal lobe (the area of visual attention, spatial orientation, and cross-modal matching)
Type of Meditation: Transcendental Meditation Technique
Neural Images: Activity in the frontal (left) increases; activity in the thalamus decreases; activity in the parietal lobe increases. 
Explanation: During the practice of the Transcendental Meditation technique, frontal lobe activity increases, and so does the parietal lobe. But the thalamus (the gateway of activation to the brain) is less active. This is called restful alertness—pure wakefulness: heightened alertness in the midst of deep silence for mind and body.
The curious reader is invited to read the complete presentation that I gave at the Science of Consciousness conference in Tucson, AZ, April 2006. The complete slideshow also explains in more detail how these three types of meditation compare in terms of brain metabolic rate, and in EEG patterns.
Meditations differ in procedure, in patterns of brain blood flow, brain metabolic rate and EEG patterns. They also differ in reported benefits. One cannot generalize the effects and benefits of one meditation to all meditations.
1. Meditation in the Tibetan Buddhism Kargyu tradition has been described as: “Reasoned deconstruction of the reality of objects experienced in meditation, as well as concentrative practices to create moods such as “pure compassion,” “loving kindness” or “no self.” This involves focused attention, and control of the mind. It is a system of concentration.
2. Mindfulness Meditation is described by Paul Grossman as “Systematic procedure to develop enhanced awareness of moment-to-moment experiences.” Mindfulness includes two meditation practices: with eyes closed: attention on breath, and with eyes open: “dispassionate observation of body, senses and environment.” This meditation involves intention or directing of attention to physiological rhythms, inner thoughts, sensations or outer objects.
3. EEG (electroencephalogram) tests show that TM is effortless because it is quickly mastered (there is no difference during the practice of TM in the EEG of someone who has been practicing regularly for 10 years versus someone who has been practicing regularly for 4 months). However, the waking state EEG of these subjects are distinctly different (the more months or years the subject has been practicing the TM technique, the more coherent their EEG pattern while resting with their eyes open).
4. Lazar, S. W., Kerr, C. E., Wasserman, R. H., Gray, J. R., Greve, D.
N., Treadway, M. T., McGarvey, M., Quinn, B. T., Dusek, J. A., Benson, H., Rauch, S. L., Moore, C. I. & Fischl, B. (2005). Meditation experience is associated with increased cortical thickness. Neuroreport, 16, 1893-7.
5. Newberg, A., Alavi, A., Baime, M., Pourdehnad, M., Santanna, J. & d’Aquili, E. (2001). The measurement of regional cerebral blood flow during the complex cognitive task of meditation: a preliminary SPECT study. Psychiatry Research, 106, 113-22.
6. Newberg, A., Travis, F., Wintering, N., Nidich, S., Alavi, A. & Schneider, R. (2006). Cerebral Glucose Metabolic Changes Associated with Transcendental Meditation Practice. Spring meeting, Neural Imaging, Miami, Fl.
Comparing The Neural Images Of Three Different Types Of Meditation.