The ability to differentiate post-cancer from healthy tongue muscle coordination patterns is necessary for the advancement of speech motor control theories and for the development of therapeutic and rehabilitative strategies. A deep learning approach is presented to classify two groups using muscle coordination patterns from magnetic resonance imaging (MRI). The proposed method uses tagged-MRI to track the tongue's internal tissue points and atlas-driven non-negative matrix factorization to reduce the dimensionality of the deformation fields. A convolutional neural network is applied to the classification task yielding an accuracy of 96.90%, offering the potential to the development of therapeutic or rehabilitative strategies in speech-related disorders.