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To clarify, are you using Latex or pdfLatex? My experience with eps files that is, for pdfLatex, the images must be converted to pdf first. See this question for more detail: Why can't pdflatex print EPS figures? If you are using pdfLatex, you can either output pdf files from Matlab or try adding the following to your preamble: \usepackage{epstopdf}

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