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The objective of this work is to compare the results obtained from the motion analysis of tagged vs. CINE MR sequences when using spatio-temporal non-rigid registration techniques based on pixel intensity. Those techniques have been previously validated on tagged MR images. Moreover, registration algorithms have been applied to MR CINE sequences to obtain radial displacement and strain parameters demonstrating its usefulness to quantify regional myocardial function. Tagged and CINE MR short axis sequences from 10 subjects were examined. Four segments were manually selected in both the tagged MR and CINE sequences. Automatic estimation of the myocardial motion field was performed using a consecutive non-rigid registration algorithm based on a semilocal Bspline parametric model. Finally, a statistical analysis was applied to compare the systolic displacement and strain estimations from both types of sequences. An important discrepancy between results obtained from tagged MR based strain analysis and CINE MR has been found.