Objective: To develop a method to quantify strain fields from in vivo intestinal motility recordings that mitigate accumulation of tracking error. Methods: The deforming geometry of the intestine in video sequences was modeled by a biquadratic B-spline mesh. Green-Lagrange strain fields were computed to quantify the surface deformations. A nonlinear optimization scheme was applied to mitigate the accumulation of tracking error associated with image registration. Results: The optimization scheme maintained the RMS strain error under 1% and reduced the rate of strain error by 97% during synthetic tests. The algorithm was applied to map 64 segmental, 12 longitudinal, and 23 propagating circular contractions in the jejunum. Coordinated activity of the two muscle layers could be identified and the strain fields were able to map and quantify the anisotropic contractions of the intestine. Frequency and velocity were also quantified, from which two types of propagating circular contractions were identified: (i) $-\text{0.36}\pm \text{0.04}$ strain contractions that originated spontaneously and propagated at $\text{3} \pm \text{1}$ mm/s in two pigs, and (ii) cyclic propagating contractions of $-\text{0.17} \pm \text{0.02}$ strain occurred at $\text{11.0} \pm \text{0.6}$ cpm and propagated at $\text{16} \pm \text{4}$ mm/s in a rabbit. Conclusion: The algorithm simultaneously mapped the circular, longitudinal activity of the intestine with high spatial resolution and quantified anisotropic contractions and relaxations. Significance: The proposed algorithm can now be used to define the interactions of muscle layers during motility patterns. It can be integrated with high-resolution bioelectrical recordings to investigate the regulatory mechanisms of motility.