Meditation is a tool of Yoga.
Yoga is defined as the cessation of the modification of Chitta, that is the cessation of the thought waves at the level of Chitta.
Activity of thr Brain is the mind, which is akin to CPU that receives inputs with no say in choosing stimulii/action..
Intellect is the instrument which decides what is correct/incorrect,Right/Wrong.
Higher than this is Chitta which guides the Intellect as to what to do in tune with the natural disposition of the individual.
As thoughts are innumerable, control over thoughts becomes difficult.
To control thoughts medi is used.
In this process , the brain is slowly guided into moving to Delta wave zone.( we normally operate on Alpha-waking,Beta,sleeping,Theeta,deep sleep).
At this level, the mind is divested of all multifarious thoughts and remains fixed on a single thought.
This changes the structure of the Brain.
Story:
Participating in an 8-week mindfulness meditation program appears to make measurable changes in brain regions associated with memory, sense of self, empathy and stress. In a study that will appear in the January 30 issue of Psychiatry Research: Neuroimaging, a team led by Massachusetts General Hospital (MGH) researchers report the results of their study, the first to document meditation-produced changes over time in the brain’s grey matter.
http://www.physorg.com/news/2011-01-mindfulness-meditation-brain-weeks.html
Meditation group participants reported spending an average of 27 minutes each day practicing mindfulness exercises, and their responses to a mindfulness questionnaire indicated significant improvements compared with pre-participation responses. The analysis of MR images, which focused on areas where meditation-associated differences were seen in earlier studies, found increased grey-matter density in the hippocampus, known to be important for learning and memory, and in structures associated with self-awareness, compassion and introspection. Participant-reported reductions in stress also were correlated with decreased grey-matter density in the amygdala, which is known to play an important role in anxiety and stress. Although no change was seen in a self-awareness-associated structure called the insula, which had been identified in earlier studies, the authors suggest that longer-term meditation practice might be needed to produce changes in that area. None of these changes were seen in the control group, indicating that they had not resulted merely from the passage of time