I've fixed this problem (which also affected 3dLRflip, 3dAnatNudge, and 3dTagalign). The source code is now on the Web site. I'm recompiling binaries now, but they take a while (there are 7 binary packages to make). Should be available this afternoon sometime (Linux first, Mac second, Solaris third, SGI fourth).
The problem was that these programs read in a dataset, modify it in memory, change its name, then write it out again -- they do not create a new dataset from scratch in memory. This is an easy programming style, but runs into trouble in your case, since the AFNI programs can't write a dataset that is marked as being stored in the MINC way. So the write operation fails (silently). The fix was one line of code in each program, just to re-mark the dataset as being stored in the AFNI way before the write operation.
bob cox
