Recently developed entrainment software has been designed to correct specific imbalances in hemispheric activity associated with undesirable mind-states. For example, people suffering with depression often have more activity in the right hemisphere, and specially designed brainwave music decreases this activity while increasing activity in the left hemisphere, reducing depression.
If brainwave entrainment leaves you with unwanted side-effects (see below) or discomfort, you’re probably encouraging a range of brainwaves that are already excessive in some area of your brain. The way around this is to get a brain map to see what your brain’s strengths and weaknesses are, and see what (if any) brainwaves could use some encouragement. 
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