So, when you overlay the two data sets ("summer" and "winter"), you can see blocky parts in one sticking out of the other?

Is it possible that the SUMA environment file is different now? I wonder if the same underlying blockiness might just *look* different because the 'shadowing' by either "modulation by background intensity" (toggled by hitting the 'a' key when the SUMA window is in the selected forefront) and/or the "background colors" (toggled with the 'b' key).

To actually change the smoothness of the output mesh, when you run IsoSurface, you can control smoothing of the regions with "-Tsmooth KPB NITER":

-Tsmooth KPB NITER: Smooth resultant surface using the Taubin smoothing
                         approach in SurfSmooth and with parameters KPB and 
                         NITER. If unsure, try -Tsmooth 0.1 100 for a start.

--pt