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If scaling of displacements to physical units does not work in Ncorr_post, the problem might be in Matlab's "ginput2.m". It helps to comment out the "if" block starting at line 611 (if all((lim~=zlim))...). Sorry for the inconvenience. 

Download: Ncorr_post v2.0 - zip
If you use Ncorr_post in your research, please cite the following paper: http://www.sciencedirect.com/science/article/pii/S0950061816305517