The person wanted to do something or act in a certain way, but was prevented from doing so by some physical aspect of his or her body. For example, someone who must use a wheelchair or who is confined to bed and who wants to run through a field may feel trapped in her own body. But it doesn't have to be a physical limitation like that - a woman a hundred years ago might have wanted to be a physician, but that wasn't seen as a common occupation for women - so she might say her dreams left her feeling trapped in her own (woman's) body.
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