I have recorded a relaxation experiment (15N CEST, Vallurupalli et al., JACS, 2012) using the NUS functionality of Topspin. The result is a pseudo-3D experiment (one "ser" file) with interleaved planes (1H-15N hsqc-like) where peaks share the same shape and position, but where their intensity differs from plane to plane. As the points were sampled randomly in both the indirect and the pseudo dimensions, each plane ends up having a different number of points.
I believe this is a similar problem to the one you dealt with in your recent paper about time-resolved NMR spectroscopy (JBNMR, 2014 ; very nice work by the way!). I tried to use qNMR to process my data, but I couldn't find a way to tell the program that the pseudo-dimension is particular and, basically, only encodes an amplitude profile for each resonance (A_i in your paper). Would you have some template files showing how to run mddnmr to process this kind of experiments?